The gas content in shale reservoir is of great importance in reservoir evaluation. Shale reservoir has various gas including free gas, adsorpted gas and soluted gas. Free gas take an important part for the total gas content. Hence, we investigated three equations for water saturation calculating and compared and improved them based on theoretical analysis in order to find a siutable one for the shale reservoir characterization. The results indicate that the Archie formula has several limitations applied to complex pore structure, which leads to high water saturation. Since the Archie formula was proposed by experimental data in pure sandstone without enough consideration about the clay of shale reservoir. The Waxman-Smits is suitable to shale gas reservoirs through theoretical analysis, but there are several uncertain parameters. The conductivity of formation water is necessary parameter in calculation of formation water saturation, but calculating the conductivity of formation water is difficult in shale gas reservoir because of its intricate characterization of pore structure and conductivity. Waxman-Smits model take account for the clay conductivity, but there are several uncertain parameters which are hard to obtained, resuting high error. For instance, the equivalent conductivity of exchange cations (B) and the capacitance of exchange anions (Qv) can not be defined accurately relied on experimental calculation, which causes indefinite influence on results. Thus, we concluded that selecting the improved Indonesia equation is a better method to calculate water saturation. This study provided a comprehensive analysis and an accurate way for water satruartion evaluation in shale reservoir.