If you have low self esteem and somebody says something nice about you, your instinctive reaction is probably that you don't believe them. You will either assume that they are stupid or weird, or you will think that they are not seeing the real you, or you will believe they are trying to flatter you because they want something.
Your reaction will probably be to put yourself down in some way. This puts them down too, because you are basically telling them they are wrong to like whatever it was that they just complimented you on.
Try just saying "Thank you" and nothing else. If you do this, you are not trying to stop them from liking you. You are saying that you respect their opinion. You might also come to believe it: and then you will no longer have to rank yourself among the many thousands or millions with low self esteem.