Organic matter is the material basis of shale gas. The Qaidam Basin is a key exploration and development area for shallow biogenic shale gas in China. In this study, we have focused on Quaternary Pleistocene shale in the Qaidam Basin, and the mechanism of organic matter enrichment was investigated in terms of water column stratification and paleoclimate. The results show that the K9–K7 section has greater biological productivity than the K5–K4 section. During the early–middle Pleistocene (K9–K7 deposition period), due to a warm and humid climate, the water column was strongly stratified and herbaceous plants developed, resulting in increased biological productivity. Stronger stratification also led to a reducing environment in the lower layer, which was conducive to the preservation of organic matter from the upper layer. During the late Pleistocene (K5–K4 deposition period), with a dry and hot climate, stratification became weaker and the vegetation evolved into woody plants, reducing biological productivity. Weaker stratification led to destruction of the reducing environment, which was not conducive to enrichment of the sedimentary organic matter. Moreover, the increased temperatures increased the activity of methanogenic bacteria, which consumed a lot of the organic matter.