Improving the resolution and accuracy of the mechanical properties of organic-rich shale is very important. The results can reveal the mechanical properties of shale from micro scale and serve as a guide for the design of hydraulic fracture optimization parameters. This study introduced an advanced technique to obtain the mechanical properties of shale with high resolution (58.6 nm/pixel) by combining SEM, EDS, and Atomic Force Microscopy (AFM). To locate the target area in SEM and AFM accurately, a positioning technique that uses special distributions of pyrite was established. AFM PeakForce QNM mode was selected due to its advantages at capturing topography and mechanical properties in material. Results illustrated the ability of AFM to obtain the mechanical properties (modulus) of individual mineral components in shale, the detailed topography of crack, and mechanical properties of minerals in a specific area. In particular, the mechanical properties of minerals around crack explained the layered distribution of minerals around the fractures, and the cracks developed in the clay mineral layer was detected. This article demonstrates the great potential application of AFM in shale.