this pen doesn't have a refill, why this sentence is right, when pen is third person,

This pen doesn't have a refill. Yes! It's right because we don't use "has" to frame a negative or interrogative sentence as a main verb. This type of sentence, we generally use "have" as a main verb because "have" is the first form of verb and we use "the first form of any verb" for framing a negative or interrogative sentence.