一般用I think it isn't funny还是I don't think it is funny.为什么?两者意思一样啊

用第二种。因为think的否定就是否定转移。在think上否定实际上是否定后面的从句。

用I don't think it is funny
当think, believe, suppose, imagine, expect等动词后接的宾语从句为含有not的否定句时，该否定应移至主句，即否定主句的谓语动词。
例如：
I don't think it will rain tomorrow.
We don't expect our football team will win the World Cup.
但hope后接的宾语从句的否定不需要转移。例如：
I hope you weren't ill.
需要特别说明的是：涉及到转移的只是not，not以外的其它否定词，如no, never, hardly, few, little, seldom等，不必转移。例如：
I believe my brother has never been late for school.
We can imagine birds can hardly live without these woods.

后者,才地道.英文中I think后面如果是否定的含义,都是用I don't think,极少用前面的说法.

用后者，这是出于习惯