It has a white highlight, that I don't like, with blond highlights. The brown roots are nice. Or write the first as "It has white highlights, that I don't like, with blond highlights. But both way are a bit unclear to me. I think "It has white highlights, that I don't like, and blond highlights. The brown roots are nice. sounds a bit clearer to me, Using "with" make me wonder if it is the white highlights that has blond highlights or if "it" has both blond and white highlights.

The sentence is confusing because you've set it up as a contrast between two things (highlights and roots) and then saying two different things about the one of those categories (I like some highlights. I don't like the others.) I would clearly separate the sentence into "things I like" and "things I don't like," since I think that's your point, rather than having the two categories be "highlights" and "roots." Your meaning will come across more clearly: "While I like the brown roots and blonde highlights, I don't like the white highlights." I hope that helps!

To me, it sounds like you don't like the white highlights WITH the blond highlights - the combination. You think that the white highlights look bad with the blond highlights. The white highlights might therefore look OK by themselves or with other highlights. The brown roots are unrelated to the highlights. Just say exactly what you say here: I like the blind highlights with the brown roots. I don't like the white highlights. It's very clear.

I like the brown roots with the white highlights, but I don't like the blonde highlights.