Structure of Cu ions in (Cl+Cu)-, (Br+Cu)-, (I+Cu)-, (S+Cu)- and (Se+Cu)-ion implanted silica glasses has been studied by x-ray absorption and optical absorption spectroscopies. Cu ions formed Cu-O bonds in the as-implanted glasses, due to the homogeneous distribution of Cu ions and the low local concentration of halogen and chalcogen ions in silica glass. Heat treatment at about 600°C caused the formation of bonds between Cu ions and halogen/chalcogen ions without forming Cu halide or chalcogenide crystals. It was deduced that the formation of these bonds was controlled by the diffusion of Cu ions in silica glass. On the other hands, it was inferred that the formation of Cu halide and chalcogenide crystals was controlled not only by the diffusion of halogen/chalcogen ions but also by the diffusion of matrix ions.