MICP is an emerging environmentally friendly sand reinforcement technique in the field of geotechnical engineering that can be used to improve the engineering performance of calcareous sands. However, due to the complex structure of MICP-treated calcareous sand specimens, more work needs to be carried out at the fine-scale to explain the macroscopic phenomena. This paper employs CT scanning to perform three-dimensional reconstruction of MICP-treated calcareous sand specimens before and after triaxial compression, and analyzes the fine-scale changes of the specimens. The results show that the two-dimensional grey-scale images obtained using CT scanning can demonstrate the pore distribution of the specimen, and the non-local mean filtering algorithm has a good noise reduction effect in the reduction process of the 2D grey-scale images. Based on this, 3D reconstruction was conducted on the MICP-treated calcareous sand specimens. The results showed that before loading, the pores of the specimens mainly distributed at one-third, two-thirds, and both ends of the specimens in the vertical direction, and the pores in these parts of the specimens would increase after loading. It is indicated that the damage to the specimen during loading mainly concentrated in the existing weak areas of the specimen itself. Segmentation of significant damage surfaces on the basis of 3D reconstructions shows that the damage mode of the specimen at low stress levels is X-conjugate shear damage, while at high stress levels the damage mode is of single bevel shear damage.