The sedimentary environment governs the depositional processes, ecological environments, and hydrodynamics, which affect the accumulation of organic-rich sediments. Some particular issues are unsolved about the organic matter accumulations of lacustrine shale mixed with shell bioclasts due to their alternating deposition. Freshwater bivalve remains are a familiar constituent of the Da'anzhai lacustrine calcareous shale, which indicates enhanced activities of benthic organisms. Under this background, favorable environmental conditions for the deposition and preservation of abundant organic matter may be different from classical models. Total organic carbon and elemental concentration analyses of lacustrine calcareous shale samples from the Jurassic Da'anzhai Member in the Sichuan Basin were carried out to reconstruct the paleoenvironment and reveal the organic enrichment mechanism. Results show that the samples are notably enriched in strontium, phosphorus and biogenic calcium (indicated by excess calcium concentrations) and reveal the mass death event of benthic organisms (including freshwater mussels and gastropods) in paleolakes under the control of climatic transformation. Such enrichment strongly supports the hypothesis that CaO is considered to be a paleoproductivity proxy to some extent. The paleolake was dominated by a warm and humid climate and rapid sedimentation rates and experienced intense chemical weathering, which are characteristic of freshwater input and a high flux of detrital fractions. The variations in the redox state and paleoproductivity are due to climatic shifts, hydrographic restrictions and biological behavior. Furthermore, the organic matter was enriched during both oxygenated and oxygen-deficient conditions. The combination of high sedimentation rates and high sinking influxes of particulate organic carbon reduced the chances of decomposition and thereby facilitated the efficiency of organic matter accumulation in an oxic environment. The low degree of organic matter degradation, moderate sedimentation rates and enhanced phosphorus recycling were responsible for the organic carbon accumulation and preservation in sediments for dysoxic bottom conditions.