The characterization of shale micropore structure and micromechanical properties is of great significance to shale gas reserve evaluation and fracturing plan design. The mechanical properties such as Young's modulus and hardness of the Longmaxi shale were tested by dot matrix nanoindentation measurements. The characterization of pore structure and the minerals of the indentation were analyzed by scanning electron microscopy (SEM) and energy dispersive X-ray spectroscopy (EDS). We established the correlation between mineral composition-nanoindentation topology and the displacement load curve. The influence of pore/fracture on nanoindentation was studied by finite element analysis. A method for evaluating shale porosity based on the displacement-load curve is proposed. Mori-Tanaka and dilute methods are used to upscale the results of nanoindentation. The main conclusions are as follows: The relationship between the pop-in characteristics of the displacement-load curve and the horizontal pores, mixed pores and vertical pores is clarified, and the elastic modulus of the rock where the horizontal pores are developed is small. A method for evaluating shale porosity based on the displacement load curve is proposed, and the calculation result is close to its macroscopic porosity of 2.64%. The Longmaxi shale has strong heterogeneity in its micromechanical properties, with Young's modulus ranging from 22.5 to 51 GPa, with an average of 41 GPa, and hardness ranging from 0.53 GPa to 2.25 GPa, with an average of 1.30 GPa. The upscaled calculation value of the dilute method is closer to the uniaxial compression value of shale. The research results are expected to accurately characterize the pore structure and micromechanical characteristics of shale and provide basic theory and scientific basis for shale fracturing design.