Microbial induced calcium carbonate precipitation (MICP) is widely common in nature, which belongs to biomineralization, and has been explored carefully in recent decades. The research studied the main factors including temperature, initial pH value and Ca2+ concentration on bacterial growth and carbonic anhydrase activity by Bacillus mucilaginosus producing extracellular carbonic anhydrase, and revealed the biomineralization process of MICP by Ca2+ concentration and calcification rate in alkali environment. Meanwhile, microbial healing agent containing spores and calcium nitrate was prepared for the early age concrete cracks. The self-healing efficiency was assessed by crack closure rate, water permeability repair rate, healing depth and so on. Moreover, the precipitations generated at the crack mouth of specimens were analyzed by scanning electron microscope (SEM) equipped with an energy dispersive spectrometry (EDS), and X-ray diffraction (XRD). After 28 d healing time of dry-wet cycles, compared with reference, the crack closure rate with the crack width up to 0.339 mm could reach 95.62%, the water permeability repair rate was 87.54%. In addition, the precipitations generated were most at the crack surface, with the increase of the crack depth, the precipitations gradually decreased. XRD analysis showed that the precipitations at the crack mouth were calcite CaCO3. Meanwhile, the self-healing mechanism of mortar cracks was discussed in detail. What’s more, the CA produced by the bacteria could accelerate the hydration of CO2 in the air, and the mineralization reaction efficiency was also high. In particular, there is no other pollution in the whole mineralization process, and the self-healing system is environmentally friendly, which provides a novel idea and method for the application of microbial self-healing concrete.