In view of the difficulty in obtaining the mechanical properties of shale, the multi-scale analysis of shale was performed on a shale outcrop from the Silurian Longmaxi Formation in the Changning area, Sichuan Basin, China. The nano/micro indentation test is an effective method for multi-scale mechanical analysis. In this paper, effective criteria for the shale indentation test were evaluated. The elastic modulus was evaluated at a multi-scale and the engineering validation of drilling cuttings was performed. The porosity tests showed that the pore distribution of shale from the nano-scale to macro-pore could be better displayed by the nuclear magnetic resonance test. The micro-scale elastic modulus and hardness increased nonlinearly with the increase in the clay packing density. It was observed that the size effect of the micro-hardness was based on porosity and composition. The partial spalling of shale at the micro-scale could lead to irregular bulges or steps in a load–displacement curve. The elastic modulus of pure clay minerals was 24.2 GPa on the parallel bedding plane, and 15.8 GPa on the vertical bedding plane. The contact hardness (pure clay minerals) was 0.51 GPa. The indentation results showed that the micro elastic modulus of shale obeyed the normal distribution, and the statistical average could predict the macro mechanical properties effectively. The present work provides a novel idea regarding the cognitive mechanics state of shale in the formation.