Undiscernible faults on seismic reflection profiles are referred to as subseismic faults. Although most subseismic faults are undetected, they play a significant role in understanding regional tectonic evolution and can influence the flow of oil and gas. The Songliao Basin in northeast China is a typical Meso-Cenozoic continental petroliferous basin characterized by stable sedimentation, rift-depression dual structure, and large-scale oil and gas production. However, the characteristics of subseismic faults and their effect on petroleum resources remain not well understood. We have examined findings from the SK-2 east borehole located in the Songliao Basin, which is the deepest (7018 m deep below the ground surface) continental scientific drilling borehole in East Asia. We identified 46 subseismic faults at 2900–4200 m depths based on the observations of core-scanning images, macro- and microstructures, and well-logging data. Macro- and microstructural analyses indicate that most of the subseismic faults in the borehole indicate normal slip. These observations suggest that these subseismic faults may form in response to regional extension in the Shahezi (K1sh) period. The cross-cutting relationships among several groups of sheared fault planes or elongated veins filled in the fractures likely reflect multistage faulting. The subseismic faults are considered to be related to the nearby larger scale faulting as interpreted on the seismic profile. The spatial correlation between the observed subseismic faults and elevated hydrocarbon concentrations documented by borehole mud gas logging suggests that the subseismic faults might have controlled gas migration in the study area.