In this paper, we have developed a new and pragmatic technique to quantitatively characterize silica content of shale of various origins. By comparing the genesis of silica in shale (i.e., biogenic origin, terrigenous origin, and clay transformation), the corresponding silica content per unit volume is determined as a function of the total silica content, each of which is determined from core samples. Subsequently, we proposed a new inverse framework and successfully applied it to quantify different types of silica in the Silurian Longmaxi formation shale in the Zhaotong area. The biogenic silica content per unit volume is found to be up to 5.61–5.67 wt%, accounting for 12.8–14.5 times of abiogenic silica, which is around 0.39–0.44 wt%, indicating that biogenic silica contributes more to the total silica than that of abiogenic silica in the bottom of Longmaxi formation. Using well logging data, the biogenic silica content is found to follow the same pattern as the total silica content in the vertical direction. Such an identified pattern together with the silica content leads to more accurate determination of porosity and more appropriate placement of a horizontal well with multistage fractures in a shale gas reservoir.