Pores within organic matter (OM) are strongly linked to hydrocarbon generation and primary migration in fine-grained source rocks and are very important for evaluating hydrocarbon storage and flow in shale reservoirs. Thus, it is critical to clarify the features of OM-hosted pores and their evolution in organic-rich mud rocks. The OM in mud rocks, including kerogen and bitumen, is deformed when the original equilibrium stress conditions are altered. The OM deformation at the nano- or microscale has rarely been discussed because of the lack of unequivocal evidence. This research begins with examining the subsurface evolution of kerogen and bitumen, with emphasis on various features of pores hosted by bitumen. Evidence of OM deformation is documented in scanning electron microscope images of seven overmature samples from the lower Silurian Longmaxi Shale, Sichuan Basin. To aid in the understanding and analysis, OM deformation is classified into three types: type I deformation induced by one additional force, type II deformation induced by two additional forces acting on two locations of single OM particles, and type III deformation induced by three or more deforming forces acting at three or more locations of single OM particles. Thus, type I deformation is generally less complex than type II and III deformation. The OM particles subjected to type I deformation were analyzed quantitatively for parameters such as pore size, geometry, and long-axis orientation of elliptical pores. Deformation of OM enhances the robust heterogeneity of OM-hosted pores.