In order to prevent structural damage or high repair costs caused by concrete crack propagation, the use of microbial-induced CaCO3 precipitation to repair concrete cracks has been a hot topic in recent years. However, due to environmental constraints such as oxygen concentration, the width and depth of repaired cracks are seriously insufficient, which affects the further development of microbial self-healing agents. In this paper, a ternary microbial self-healing agent composed of different proportions of Bacillus pasteurii, Saccharomyces cerevisiae, and Bacillus mucilaginosus was designed, and its crack repair ability was evaluated. When the mixing ratio was 7:1:2, the cell concentration was the highest, the precipitation amount of CaCO3 was the highest, and the crystallinity of calcite crystal was the highest. Compared to the single microorganism, the mortar specimens with ternary microorganisms had the largest repair area (up to 100%) and the deepest repair depth (CaCO3 presents at 9–12 mm from the crack surface). This is because when the concrete breaks, all three microorganisms are activated by water, O2, and CO2. Saccharomyces cerevisiae and Bacillus mucilaginosus accelerated the growth of Bacillus pasteurii and more mineralized products; CaCO3 was rapidly formed and quickly filled on the crack surface. When CaCO3 seals the surface of the crack, the internal Saccharomyces cerevisiae and Bacillus mucilaginosus continue to play a role. Bacillus mucilaginosus can accelerate the dissolution of CO2 produced by the anaerobic fermentation of Saccharomyces cerevisiae and the hydrolysis of CO32−, thereby improving the repair of the crack depth direction.