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The lacustrine oil shales of the Youganwo Formation in the Maoming Basin, as an excellent continental sedimentary record of the middle Eocene, provide an interesting perspective for understanding the middle Eocene paleoclimate and organic matter (OM) accumulation in south China. Based on detailed organic petrology and geochemical analysis of the Jintang oil shales (JTOS) and the Yangjiao oil shales (YJOS), the paleoenvironment during the middle Eocene in South China was reconstructed, and control OM accumulation in the oil shales was revealed. These oil shales are characterized by high OM abundances (TOC: 8.2–21.4 wt %), kerogen types of I and II1, and are in the immature stage. The source OM was predominantly lacustrine endogenous OM (algae and bacteria). Element ratios (Sr/Cu, Fe/Mn, and Si/Al) indicate a warm paleoclimatic background during deposition of the Youganwo Formation, which is related to the Mid-Eocene Global Climatic Optimum. Representative indicators (Sr/Ba, 100*Mg/Al, Pr/Ph, DBT/P ratios; the covariant MoEF–UEF pattern) show that anoxic fresh water is dominant during the deposition of the Youganwo Formation. Sufficient nutrient supplies (P, Fe, Mn, Cu, etc.) were conducive to the flourishing of algae, which led to high lake bioproductivity. The relationships between the TOC content and paleoenvironmental indicators show that high bioproductivity and strong anoxic conditions are conducive to the formation of high abundance OM in the JTOS, whereas the dilution effect induced by the enhanced terrigenous detrital input reduced the OM accumulation in the YJOS. The comprehensive model of the paleoenvironment and OM accumulation further shows that under warm and humid climates, the dominant roles of bioproductivity and the important role of preservation conditions controlled OM accumulation in the oil shales in the Maoming Basin.