In organic-rich lacustrine shales subjected to volcanic or hydrothermal activity, the transformation and dissolution of zeolites are key to the formation of high-quality reservoirs. Some reservoirs in eastern China contain a large amount of analcime (content up to 59%), which records complex depositional and diagenetic evolution processes. Based on detailed petrographic investigation, in situ element measurement, and organic geochemistry analysis, the significance of analcime for reservoir modification, hydrocarbon migration, and accumulation was investigated in the second member of shales from the Paleocene Kongdian Formation of the Bohai Bay Basin. The study characterized two analcime laminae assemblages (analcime-clay lamina assemblage [ACL] and “analcime+calcite”-clay lamina assemblage [A-CCL]) and their vertical distribution patterns. For the ACL, the mixture of silica-rich hydrothermal fluids and highly alkaline lake water induced illite-to-analcime transformation. For the A-CCL, the anorthite in the plagioclase sequence gradually transformed into albite, acting as an intermediate in the calcite-to-analcime transformation. The influence of analcime on thermal evolution and hydrocarbon migration is controlled by Si/Al and its association with organic matter. High-silica analcime lamina in ACL are coprecipitated with organic matter and exhibit continuous, stable catalytic effects on hydrocarbon generation processes. Low-silica analcime lamina in A-CCL show no coprecipitation with organic matter but create intergranular pores through synergistic diagenetic alteration with calcite and clay minerals, forming effective reservoir storage spaces. The low-silica fracture-filled analcime enhances hydrocarbon cracking efficiency and undergoes dissolution by organic acids, creating effective migration pathways. The synergistic interplay between distinct analcime morphologies and organic constituents constitutes a critical control on premium reservoir formation.