Hi Daxi
Goodman well explained about the semantic difference of the two sentences. I'd like to add some grammatical difference between the two.
[1]What do you think about/of it?
Here "think" (=deduce, infer) is a transitive verb and "what" is the direct object of "think". And "about/of it" could be taken as an adverbial phrase to indicate the range of "think" or the material of "think".
[2] What are you thinking about?
Here "think" (=mediate, ponder) is an intransitive verb. "What" is the object of the preposition "about".
paco