Cuando me duelen los ojos, me cuesta parpadear.

Spanish often talks about body parts differently from English.

Instead of saying my eyes hurt, Spanish usually says something closer to the eyes hurt to me:

• me = to me
• duelen = hurt
• los ojos = the eyes

So me duelen los ojos is the natural Spanish way to say my eyes hurt.

Using mis ojos duelen is grammatically possible in some contexts, but it sounds much less natural for ordinary physical sensations.

Because the subject is los ojos, which is plural.

The verb doler agrees with the thing that hurts, not with the person affected.

• Me duele el ojo = My eye hurts
• Me duelen los ojos = My eyes hurt

So:

• el ojo → singular → duele
• los ojos → plural → duelen

Here me is an indirect object pronoun, meaning to me.

It shows who is affected by the pain.

Examples:

• Me duele la cabeza = My head hurts
• Te duelen los pies = Your feet hurt
• Le duele la espalda = His/her back hurts

So in me duelen los ojos, me does not mean myself in a reflexive sense. It means to me.

With body parts, Spanish usually prefers:

• an indirect object pronoun: me, te, le, nos, os, les
• plus the definite article: el, la, los, las

So Spanish says:

• Me duelen los ojos literally: The eyes hurt to me

rather than:

• Mis ojos me duelen

This is one of the most common patterns in Spanish for body parts and physical sensations.

Cuando means when.

In this sentence, it introduces a general or repeated situation:

• Cuando me duelen los ojos, me cuesta parpadear.
• When my eyes hurt, blinking is hard for me.

Because it describes something that generally happens, Spanish uses the present tense in both parts.

If you were talking about a specific past event, you would normally use past tenses instead:

• Cuando me dolían los ojos, me costaba parpadear.

Literally, it means something like:

• it is difficult for me to blink
• or blinking costs me effort

The verb costar can mean to cost, but it is also very commonly used to mean to be difficult.

So:

• Me cuesta parpadear = It’s hard for me to blink

Other examples:

• Me cuesta dormir = It’s hard for me to sleep
• Nos cuesta entenderlo = It’s hard for us to understand it

This me also means for me or to me.

In the structure costarle algo a alguien, the pronoun shows who finds something difficult.

So:

• me cuesta = it is difficult for me
• te cuesta = it is difficult for you
• le cuesta = it is difficult for him/her

The subject of cuesta is actually the action parpadear.

So the structure is basically:

• Parpadear me cuesta = Blinking is difficult for me

But Spanish normally prefers:

• Me cuesta parpadear

Because the infinitive in Spanish often works like an English -ing form or verbal noun.

Here parpadear means to blink, but in context it functions more like blinking:

• Me cuesta parpadear = Blinking is hard for me

This is very common after verbs like:

• gustar
• costar
• querer
• necesitar
• poder

Examples:

• Me gusta leer = I like reading / I like to read
• Me cuesta concentrarme = It’s hard for me to concentrate

Yes, but the meaning changes slightly.

• Me cuesta parpadear = It’s hard for me to blink
• Cuesta parpadear = Blinking is hard / It’s hard to blink

Without me, the sentence becomes more general and less personal.
With me, it clearly says that I am the one who finds it difficult.

Since the first part already talks about my eyes, both versions may be understandable, but me cuesta parpadear is more precise and natural here.

Yes. Spanish word order is flexible, although some orders are more natural than others.

The original sentence:

• Cuando me duelen los ojos, me cuesta parpadear

You could also say:

• Me cuesta parpadear cuando me duelen los ojos

That sounds natural too. The meaning stays basically the same.

What you usually should not do is move things around randomly in a way that breaks the normal pronoun-verb relationship.

Usually it sounds like a general or habitual statement:

• Whenever my eyes hurt, I find it hard to blink.

The present tense in Spanish often does that.

If you wanted to describe one specific situation happening right now, this same sentence could still work depending on context, but very often it is understood as a general statement unless the context makes it specific.

Yes, very much so. This is one of the most useful things to notice in the sentence.

All three often use a similar pattern:

• indirect object pronoun: me, te, le...
• verb agreeing with the subject that comes later

Examples:

• Me gusta el libro = I like the book
• Me duele la cabeza = My head hurts
• Me cuesta hablar español = Speaking Spanish is hard for me

So if you already know how gustar works, that will help you understand both doler and costar.

Yes, it sounds completely natural in Spain.

Nothing in the sentence is especially regional or unusual. It is standard Spanish that would be understood everywhere in the Spanish-speaking world.

If anything, it is a very useful sentence because it shows several common Spanish patterns at once:

• cuando
  • present for repeated situations
• doler with body parts
• definite article with body parts
• costar
  • infinitive for difficulty