Clay minerals in clastic sediments carry important geological information, with their composition and variations reflecting key geological processes. This study investigates the differential clay mineral assemblages among lithofacies within the Middle Jurassic continental shallow-water delta system of the Sichuan Basin, China. Integrated geochemical and XRD analyses demonstrate the significant influence of paleoclimate-driven weathering and diagenetic alteration on clay mineral assemblages. The invariant geochemical characteristics (such as Ti/Al) across different mudstone confirm a uniform provenance, establishing paleoclimate-controlled weathering processes as the principal determinant of clay mineral composition, with negligible provenance influence. Chemical weathering intensity, controlled by the depositional paleoclimate, is a primary factor influencing clay mineral composition in mudstones. In warm, humid climates, abundant rainfall and strong chemical weathering lead to kaolinite enrichment and smectite depletion in black shale facies. Conversely, in cooler, drier climates, physical weathering dominates, resulting in significant illite formation in red mudstone and paleosol facies. In sandstone facies, clay minerals are controlled by diagenetic fluid composition and flux. Chlorite content is related to the primary permeability of the sandstone, while illite content is influenced by K+ concentration in diagenetic fluids, with stronger illite enrichment in areas of intense feldspar dissolution. The smectite-to-illite transformation is common in both sandstone and mudstone facies, with its extent influenced by the openness of the diagenetic system and K+ availability. In humid conditions, feldspar dissolution in an open system leads to K+ advection into sandstone, reducing smectite-to-illite transformation in mudstones. In semi-arid conditions, feldspar dissolution occurs in closed systems during burial, with K+ diffusing into mudstones, promoting greater illitization in mudstones than in sandstones. This study provides insights into how paleoclimate and diagenesis control clay mineral transformations in sedimentary rocks.