Both these questions are normal in Russian, but there is a difference in usage.
The question with что is used when you ask to express an opinion about something. You introduce the subject with о preposition or with words like насчёт, по поводу:
Что ты думаешь о глобальном потеплении? - What do you think about global warming?
The question with как is used when you ask to make a choice of something (including questions you can answer with yes/no). There is no preposition:
Как ты думаешь, завтра будет дождь или нет? - What do you think, will it rain tomorrow or not?
Notable that use of что was normal in this case a hundred years ago or so.
When you just said something and want your interlocutor to reply in some way, both questions will work:
[А] как ты думаешь? (more usual, less formal)
[А] что ты думаешь?
If in doubt, opt for что. In the worst case you will sound old-fashioned.