In recent years，consolidating soil by the microbially induced carbonate precipitation (MICP)technique has been extensively studied in the civil engineering field. However，most of those studies focus on the macroscopic mechanical properties. Since the macro-mechanical properties are often influenced by micro-mechanical properties，the nanoindentation experiments were conducted on bio-cemented shale soil under different levels of peak load to explore the micro-mechanical properties of bio-cemented shale soil. The elastic modulus，hardness，and fracture toughness of bio-cemented shale soil were obtained based on the calculation model of elastic parameters and plastic fracture mechanics theory. To analyze the influence of the calcium carbonate crystal morphology and distribution of mineral crystals of measuring points on the micro-mechanical properties of calculus，the forms of calcium crystals were observed by using an optical microscope. Besides，the X-ray diffraction test was also conducted on bio-cemented samples to investigate the effect of mineral components in the sample on its mechanical properties. Afterward，the relationship among the elastic modulus，hardness，and fracture toughness of bio-cemented samples was analyzed. The results show that it is feasible to test the elastic modulus，hardness，and fracture toughness of bio-cemented shale soils by using the nanoindentation technique. However，there is discreteness in the values of elastic modulus，hardness，and fracture toughness of bio-cemented shale soil because the texture of calcium carbonate crystal induced by the MICP technique is inhomogeneity. In addition，the quartz in the soil with higher strength strengthens the mechanical properties of shale soils，resulting in the improvement of mechanical parameters of some shale soil particles. Moreover，the trend of fracture toughness in each region is the same as the modulus of elasticity and hardness，and there is a simple linear relationship among them. The nanoindentation technique breaks the limitation of specimen size in conventional mechanical tests. The results provide a reference for determining the micro-mechanical parameters of bio-cemented shale soils.