Microbial-induced calcium carbonate precipitation (MICP) is a new biotechnology that can be used to improve the strength of soils. Unsaturated soils are common in nature and saturation is a significant factor affecting the efficiency of bio-cementation. This study investigated the properties of MICP under different grouting saturation conditions. Unconfined compressive strength (UCS) tests confirmed that biocemented sand could get higher strength under unsaturated grouting conditions with the same calcium carbonate content which helps reduce the material cost. Scanning electron microscopy (SEM) test results show that at lower saturation, the size and amount of calcium carbonate crystals were insufficient but calcium carbonate mainly gathered between the particles. At higher saturation, larger calcium carbonate crystals were produced and exited in pores and on the particle surface, increasing the filling effect. Energy-dispersive X-ray spectroscopy (EDS) and X-ray diffraction (XRD) test results show that the dominant calcium carbonate morphology detected in samples was calcite, which was the most stable one. X-ray computed tomography (CT) test results show that after cementation, the measured contact surface area became uniform and the coordination number was higher. The flow direction of bacteria and the cementing solution did not induce significant anisotropy in the cementation process. The effective cementation and content of calcium carbonate jointly influenced the improvement of soil mechanical properties.