Silicalites are widely distributed in the Wujiaping Formation of Upper Permian in the Shizhu area, Chongqing. Through detailed field observation, combined with the data of macro-analysis, REE and isotope of silicalites, it is indicated that the silicalites of the Wujiaping Formation are characteristic of biogenesis with hydrothermal activity. There were many syn-depositional faults and volcanism in the late Permian in eastern Sichuan basin. And the heat source responsible for hydrothermal convection is presented in study area. Present studied section is just located near the Qiyaoshan fault, which could be the pass of hot liquid from deep crust. At that time, sea water encountered and was heated with magmatic liquid, and then dissolved much SiO2 and other elements. Finally, sea water enriched in SiO2 grew much better and siliceous biology died and set down to form bio-siliceous rock.