In high energy laser systems, the energy absorption rate (EAR) of mono-crystalline silicon reflector is a vital index in the term of elements quality. The substrate process quality affects the EAR of coated optics dramatically. The surface roughness and scratch density for a series of silicon optics were measured. Based on the result, the co-influence and relationship between surface characteristic and EAR were analyzed. It is indicated that, surface roughness level is positively correlated to EAR and decides the global average rate of the entire surface. When the root-mean-square of roughness falls from 0.668nm to 0.345nm, the EAR decreases by 28.0%. In contrast, few scratches do not distinctly raise the EAR, the fluctuation is less than 3.1%. However, the surface scratch may generate laser-induced damage. Furthermore, when the scratch density is large enough, the subsequent EAR will grow constantly, for example, the amplitude reaches 18.3% after the 400s irradiation, compared with 100s irradiation.