Cement-based materials are brittle and crack easily under natural conditions. Cracks can reduce service life because the transport of harmful substances can cause corrosion damage to the structures. This review discusses the feasibility of using microbial self-healing agents for crack healing. Tubular and spherical carriers can be used to load microbial self-healing agents and protect microbes, which prolongs the self-healing time. The area self-healing ratio, permeability, mechanical strength, precipitation depth method, numerical modeling, and ultrasonic method can be employed to identify the self-healing effect of cracks. Moreover, the self-healing mechanism is systematically analyzed. The results showed that microbial self-healing agents can repair cracks in cement-based materials in underground projects and dam gates. The difficulties and future development of self-healing cracks were analyzed. A microbial self-healing agent was embedded in the cement-based material, which automatically repaired the developing cracks. With the development of intelligent building materials, self-healing cracks have become the focus of attention.