Three nano-resolution petrological microtextures were discovered in the siliceous shale at the bottom of the Longmaxi Formation in the Zigong area, Sichuan Basin. Based on observations of the occurrences of the minerals, organic matter, and organic matter pores in the different microtextures and analysis of their relationships by means of nano-resolution petrological image datasets obtained using the Modular Automated Processing System (MAPS 3.18), the formation mechanism of the siliceous shale was studied. The results show that the strong modification of clay-rich sediments by a deep-water traction current was the basis for the formation of the siliceous shale. The clay-rich sediments were converted into flocculent sediments rich in oxygen and nutrients via agitation and transport by the deep-water traction current, providing space and a material basis for microbes to flourish. Under the continuous activity of the deep-water traction current, the clay-rich sediments were transformed into microbial mats, in which in situ terrigenous detrital quartz and feldspar, endogenous detrital calcite, authigenic dolomite, and dolomite ringed by ferrodolomite were scattered. During the burial stage, the microbial mats were lithified into the siliceous shale composed of three petrological microtextures. Microtexture I was mainly transformed by microbes. Microtexture II was formed via lithification of the residual clay-rich sediments. Microtexture III was composed of migratory organic matter filling hydrocarbon-generating pressurized fractures. Due to the universality of deep-water traction flow and the diversity of microbes in deep-water sediments, we firmly believe that more and more deep-water microbialites will be discovered worldwide through systematic characterization of nano-resolution petrology with the booming development of the shale gas industry.