Why is Libethenite (Cu2(OH)PO4) color green? It is not a complex compound and the copper atom is not oxidized so I'm wondering how does its color change. The book mentioned that at favorable conditions, adding water in Copper phosphate, which is blue, will result in the formation of Libethenite.
First of all, why do you think your copper is not oxidized? Each copper has a charge of +II while $\ce{OH^-}$ and $\ce{PO_4^3-}$ add up to -4. 

For all further discussions we need to look deeper into the crystal structure. The compound crystallizes with two crystallographically destinguishable copper ions. One forms a $\ce{[Cu(PO_4)_4(OH)_2]^12-}$ octahedron while the other one is, at least to me only fivefold coordinated to form a trigonal bipyramid $\ce{[Cu(PO_4)_4(OH)]^11-}$.
Of course those are no simple $\ce{OH}$ units as there is further bridging and connections happening but for a simple view this should be okay. So for the color there are, among other effects, still $\ce{d-d}$ transitions happening. 



EDIT:

To add something to the color change in the reaction itself. In your copper phosphate you have copper polyhedra that only feature phosphate as ligands, for the $\ce{[Cu_3(PO_4)_2]}$ these would be trigonal bipyramid and square plane.So you have the addition of $\ce{OH^-}$ to these polyhedra as well as some substitution. And introducing a different ligand will also change your splitting energy and therefore change the color.