The economic exploitation of unconventional gas and oil in deep shale relies closely on effective hydraulic fracturing stimulations. However, the fracturing operations of deep shale reservoirs face challenges of insufficient fracture growth and a rapid decline in productivity due to the increasing in situ stress level. In addition, the shale strata on the margin of the Sichuan Basin are frequently folded and faulted, and the change in bedding inclinations significantly complicates the process of hydraulic fracturing. The investigation of the combined effect of the in situ stress level and bedding anisotropy on the hydraulic fracture configuration is vital for fracturing engineering design. To analyze this, we conducted hydraulic fracturing tests on shale cores to simulate the hydraulic fracture initiation and growth from a horizontally positioned perforation. By using acoustic emission detection and CT scans, the influence of natural stress levels and the angle of the shale’s bedding on the process of hydraulic fracturing in shale and the resulting fracture geometry were analyzed. The results showed that the area of hydraulic fracture under a higher stress level (σ1 = 50 MPa, σ3 = 40 MPa) was about 13%~23% smaller than that created under the lower stress level (σ1 = 30 MPa, σ3 = 20 MPa) when the bedding angle was smaller than 60°. With the increase in bedding angle, the curves of the fracture area and fracture network index under two different stress levels presented similar decreasing trends. Also, the time from micro-crack generation to sample breakdown was significantly reduced when the bedding orientation changed from the horizontal to vertical position. The increasing stress level significantly increased the breakdown pressure. In particular, the fracturing of shale samples with bedding angles of 0° and 30° required a higher fluid pressure and released more energy than samples with larger bedding inclinations. Additionally, the measurement of the sample radial deformation indicated that the hydraulic fracture opening extent was reduced by about 46%~81% with the increasing stress level.