To evaluate the effects of quartz precipitation on the abundance and preservation of organic matter pores in marine shale reservoirs, the type of authigenic quartz and the source of silica, as well as the corresponding relation of the Lower Cambrian Shuijingtuo Formation shale in South China were investigated. Quartz in the Shuijingtuo shale occurs as four different types: detrital quartz, replacement of biosiliceous debris, euhedral quartz filled in interparticle pores, and microquartz dispersed in a clay matrix. Euhedral quartz (1–5 μm) and matrix-dispersed microquartz (100–400 nm) are found to be the dominant forms of authigenic quartz. The euhedral quartz accumulates along the interparticle pores, and the porous organic matter fills the interior of the space. Microquartz is mainly wrapped in porous organic matter. Two silica sources were revealed: biogenic silica and clay-derived silica. Biogenic Si is most likely the major source for authigenic quartz in the organic-rich (total organic carbon (TOC) > 2.55 wt.%) samples, which accounts for 23–57 wt.% (average 35 wt.%) of the total Si. Based on petrographic observations, we posit that the precipitation of large-sized euhedral quartz in the interparticle pores most likely originated from biogenic silica in the early stage of diagenesis and that the silica for the clay matrix-dispersed microquartz is provided by biogenic silica and clay-derived silica. The observation of SEM images indicates that the precipitation of early diagenetic euhedral quartz in the interparticle pores enhances rock stiffness, and the buttressing effect can protect the organic matter pores from compaction during the late-stage burial diagenesis. In contrast, the precipitation of late diagenetic microquartz in the clay matrix can lead to a reduction in the capacity of the accommodation space to host retained petroleum, consequently leading to a reduction in the development of organic matter pores and the generation of shale gas.