Quartz, as a pivotal constituent of shale, has garnered considerable attention in research. Nevertheless, prior studies on quartz in shale have concentrated on its influence on organic matter accumulation, pore development, and physical properties. The crystal morphology of quartz and its implications for shale reservoir performance have been largely overlooked. This study utilizes the Longmaxi (LMX) shale in the Sichuan Basin, China, as an example to conduct this work. We used X-ray powder diffraction, polarizing microscopy, scanning electron microscopy, and cathodoluminescence testing, characterizing the crystallinity and characteristics of quartz, revealing the influence of quartz crystallinity on shale reservoirs. The results indicate that the quartz crystallinity index (QCI) of the LMX shale ranges from 2.81 to 8.09, and a significant correlation between the QCI and the sources of quartz is observed. Shale samples with lower QCI values tend to exhibit a higher content of biogenic quartz, whereas the content of clay-transformed quartz and/or terrigenous detrital quartz increases. Furthermore, the pore structure parameters of shale exhibit synergistic variations with QCI, especially for shale with low crystallinity, despite showcasing differences for pores with different pore sizes. Notably, QCI exhibits the strongest negative correlation with micropores, followed by mesopores, while this correlation is less apparent in macropores. The influence of QCI on pore development is primarily ascribed to its synergistic interaction with organic matter enrichment and the constraints imposed on the development and preservation of organic-matter-hosted pores. Under the well-preserved geological conditions of the LMX shale reservoirs, a definite correlation exists between the QCI value and shale gas content/production. This correlation signifies that QCI could serve as a potential indicator for assessing shale reservoir quality, complementing conventional parameters, such as the contents of total organic carbon and quartz.