Triassic mudstones in the Junggar Basin of northwest China, especially those of the Upper Triassic Baijiantan Formation, which formed during a lake-flooding event, are the most important set of cap rocks in the basin. These mudstones presumably have hydrocarbon generation potential, although this potential has not been documented. Here, we provide new organic geochemical and geological background data on these mudstones, and discuss their hydrocarbon generation potential. Geochemical analyses were performed on available samples collected from more marginal shallow-lake facies in the central basin area. These analyses indicated that these rocks contain about 1.0% total organic carbon (TOC). The organic matter type is predominantly type III kerogen derived mainly from terrestrial higher plants. The organic matter underwent maturation in uplifted areas and reached higher maturity levels in depressions within the basin. Thus, the Triassic mudstones may have a potential for hydrocarbon generation during the lake-flooding period, especially for gas, and hence deserve attention in future exploration. More research needs to be conducted on the generation potential of these units (including oil besides gas), as few deep-lake facies samples from depressions in the basin are currently available for investigation.