Organic-rich mudstone, whose formation and accumulation are strongly related to the depositional environment, is a potential source of natural gas. Here, geochemical tests (including total organic carbon (TOC), rock pyrolysis, X-ray diffraction (XRD), and main and trace element analyses) were carried out on mudstone samples from two boreholes in the Jixi Basin to reveal the paleoenvironment and its control on organic matter enrichment. The results show that type III kerogen dominated and that all samples entered the maturity stage with good hydrocarbon generation potential. Generally, the TOC content tended to increase with increasing depth, and the mudstone in the middle (K1ch2) and lower (K1ch1) segments of the Chengzihe Formation was characterized by good quality with TOC > 2.5%. In the Jixi Basin, two common types of mudstones (silica-dominated mudstone and silica-rich argillaceous mudstone) were mainly composed of quartz and clay minerals. These mudstones were rich in Na2O, MnO and several trace elements (e.g., Zn, Mo, and Bi) and depleted in other elements (e.g., MgO, CaO, Cr, Co, and Ni). The rare earth element and yttrium (REY) distribution patterns normalized by North American shale compositions (NASC) were flat, with slight negative Ce and Eu anomalies. The ratios of Sr/Cu, Rb/Sr, Sr/Ba and V/(V + Ni) in mudstones indicated a warm-humid paleoclimate, a suboxic environment and a marine-continental transitional fresh-brackish water mass. From the K1ch1 to Muling Formation (K1m), although the paleoclimate was more arid and paleosalinity increased gradually, depositional environments were in fresh-brackish water. The paleoclimate and clastic influx are the keys to controlling the enrichment of organic matter. The paleoclimate indirectly affects the preservation of organic matter by influencing the aquatic environment and controlling the level of paleoproductivity, while the strong clastic influx rate directly dilutes organic matter preservation.