As an emerging repair method, the enzyme-induced calcium carbonate precipitation (EICP) technique has the advantages of being highly economical, eco-friendly, and durable. The optimal repair conditions were obtained by taking cement mortar as the research object, adding two types of filling medium, using three EICP-based repair methods to repair the cement mortar with different crack widths, and combining ultrasonic testing and strength testing to evaluate the mechanical properties and repair effects of the repair mortar. The microscopic structure of the mortar was established using mesoscopic and microscopic tests (XRD, SEM, and EDS), thereby revealing the mechanism of repair based on EICP. The test results show that, when quartz sand is used as the repair medium, more calcium carbonate adheres to the cross-section of test samples, and it has a better repair effect. Moreover, the repair effect of the injection method is significantly higher than those of the perfusion and immersion methods, and the ultrasonic wave transit time decreases by 1.22% on average. Based on the combination of quartz sand and EICP repair methods, the calcium carbonate precipitated among the sand granules contributes to a binding effect that strengthens the cohesive force among the sand granules.