Identification of natural microfractures is important for shale reservoir evaluation. In total, 42 selected core samples from the Wufeng-Longmaxi marine shales in the Fuling gas field, southeastern Sichuan Basin, were analyzed using water-immersion testing, computed tomography scanning, and argon-ion polishing scanning electron microscope experiments, along with edge detection and image stitching analysis methods. The results indicate that the immersion experiment is an effective way to identify natural fractures. Three types of natural microfractures correspond to bubble positions with 250 nm resolution scanning electron microscopy: bedding fractures, particle edge fractures, and dissolution fractures. The bedding and dissolution fractures show the same occurrence as the strata, and they are the main bubbling channels. The occurrence of particle edge fractures varies significantly. Microfractures are capable of forming a fracture network, connecting separated storage spaces in the shale reservoir. The best fracture network is formed by bedding and dissolution fractures in 3D space. Furthermore, apportion of the particle edge and dissolution fractures is capable of forming microfracture networks in shale cores increasing the connectivity of pore spaces. The number of bubble points also indicates a positive correlation with shale laminae, which indicates that microfractures are developed mainly within the laminae. The number of shale laminae and the number of microfracture channels can be calculated quantitatively by the number of bubble points. The observations can be used in the drilling site to estimate the physical properties of shale reservoirs quickly and quantitatively.