To investigate an effect of phase separation on precipitation characteristics of CuCl nanocrystals in CuCl doped nonlinear optical glasses, borosilicate glass systems with 9 different compositions with ~2wt% of CuCl were selected and CuCl doped glasses were prepared by melting and precipitation method. Microstructural properties of the CuCl doped glasses were analyzed by optical absorption spectroscopy, acid elution test, TEM, and EDXS. While phase separation did not occur in Glass A~D, interconnected and droplet microstructures due to phase separation were found in Glass E, F and Glass G~I, respectively. In the particular composition of the matrix glasses in this study, the precipitation of the CuCl particles was observed in the phase separable glasses, not in phase non-separable glasses. The CuCl particles were precipitated in both silica-rich phase region and boronrich phase region of the glass matrix. In the case of 7.7Na2O-36.6B2O3-52.7SiO2(mole%) glass, the larger CuCl particles than those in the silica-rich phase region were observed in the boron-rich phase region.