Any theories on how he changes so fast and what exactly happens to his bones, muscles, etc ?

Why is he green?  Any theories?

Its a comic book.

"Its a comic book. "

Because there is totally logical science behind Beast Boy's powers to think about in the first place right?

hey it's totally logic that if a green monkey bites you you....nvm

The emperor from Mummy 3: Tomb of the dragon emperor was the same way, instantly changing into creatures would you rather they do it slowly? then it'd look slightly less badass

I'm just curious as to what goes on in his anatomy

in the same way Cyclops and Superman can see while using their beam vision. 
 
And how Storm can control the weather.
And Johnny Storm can shoot fire from his hands. 
 
etc etc
 
There is no real world logic behind super powers.

Here is my favorite super power that makes no sense. The whole travel back and change things. Look at people like Bishop, Cable, Dr.Doom and Lyra, they have both gone back, changed the past but yet they still remain unchanged. Wouldn't changing something in the past (especially major events like Bishop has done many times) for the most part change your or in most cases cause you to never be born in the first place. Time travel is something that can only make since in fantasy, cause when you really sit down and think about it, you head for the most part will explode.

"Here is my favorite super power that makes no sense. The whole travel back and change things. Look at people like Bishop, Cable, Dr.Doom and Lyra, they have both gone back, changed the past but yet they still remain unchanged. Wouldn't changing something in the past (especially major events like Bishop has done many times) for the most part change your or in most cases cause you to never be born in the first place. Time travel is something that can only make since in fantasy, cause when you really sit down and think about it, you head for the most part will explode. "

I suspect that his entire body converts to a homogenous organic mass nearly instantaneously, alters shape, then reconverts back into the necessary tissue and organs of the animal of choice.  Its mostly physical, but partly mental.  Its been shown that Beast Boy has to know what he's turning into, and can't just invent animals out of whole cloth. 
 
Its possible that he's subconsciously connected to the morphogenic field, like Animal Man and Vixen.

" @MrMiracle77: Morphogenic field? "