The properties of hydrogenated amorphous silicon (a-Si:H) thin layer are studied by spectroscopic ellipsometry (SE) measurement for the surface passivation of crystalline silicon (c- Si) in heterojunction solar cell. The scatter interval (St) of defect at the a-Si:H/c-Si interface, concentration of micro voids and maximum value of dielectric function of a- Si:H layers deposite at different substrate temperatures (Ts) are analyzed by fitting with multilayer mode based on the effective medium approximation. By comprising with the microstructure data calculated from Fourier transform infrared spectroscopy, the correlation between St and the H- bond configurations in a- Si:H layer is obtained. According to the measurement results of transmission electron microscope (TEM), effective minority carrier lifetime and implied open circuit voltage, it is demonstrated that SE technique is an effective characterization tool to estimate the surface passivation quality of a-Si:H for c-Si. Thus, the optimal parameters are quantitatively obtained for the deposition of high quality a-Si:H passivation layer for silicon heterojunction solar cell.