The influence of the paleoclimate on the organic matter (OM) accumulation and depositional process in the third member of the Hetaoyuan Formation shales is unclear in the Paleogene lacustrine systems in the Biyang Depression, Nanxiang Basin, Eastern China. Here, inorganic and organic geochemical analyses were performed on samples from a 25 m profile to examine the effects of paleoclimate change on the depositional environment and OM accumulation within this interval. Based on mineralogical and geochemical data from the B1 Well, two major lithofacies assemblages, calcareous mudstone-dominated (LA1) and clay-rich mudstone-dominated (LA2), were identified. Although generally anoxic bottom water was present during sedimentation, subtle differences in depositional environment and OM enrichment were found for the two lithofacies. The mineral composition and multiple geochemical proxies, including detritus index (sum of quartz, clay minerals, and feldspar contents), C-value [∑(Fe + Mn + Cr + Ni + V + Co)/∑(Ca + Mg + Sr + Ba + K + Na)], chemical index of alteration (CIA = 100 × Al 2 O 3 /(Al 2 O 3 + CaO* + Na 2 O + K 2 O), Rb/Sr, V/(V + Ni), Sr/Ba, Pr/Ph, and gammacerane/C 30 hopane ratios all indicated that LA1 was deposited in a stable stratified saline lake with anoxic bottom water in a relatively cool, arid paleoclimate. However, these parameters suggested that LA2 was deposited in a brackish-to-saline lake with anoxic bottom water in a relatively warm, humid paleoclimate. Abundant OM (average total organic carbon (TOC) content 4.24 wt %) was accumulated mainly in LA1, with relatively high primary productivity suggested by high values of P/Ti, Ba/Al, 4-methylsterane/∑C 29 steranes index (4-MSI), ααα20RC 27 /ααα20RC 29 sterane (C 27 /C 29 ), and ααα20RC 28 / ααα20RC 29 (C 28 /C 29 ) sterane ratios. In contrast, in warmer, more humid conditions, the corresponding sediments in LA2 contained less OM (average TOC 2.29 wt %), consistent with ratios indicating lower primary productivity and higher detritus input. We draw the conclusions that the accumulation of higher OM in LA1 was controlled by the combination of paleoproductivity and preservation in anoxic bottom water, while the formation of the LA2 organic-rich mudstone was mainly related to primary productivity, anoxic conditions, and the dilution by terrigenous detrital matter.