The seepage of sandy foundation would lead to the collapse of foundation and the destruction of engineering structure. A series of large-scale sand column seepage model experiments was carried out by using microorganism–bentonite combined mineralization method. The in-depth discussion was conducted for the effects of sand particle size, slurry liquid-to-solid ratio and treatment cycles on the permeability, internal erosion characteristic and bentonite and calcium carbonate precipitate distribution of sand. Moreover, the stability of sealing and the microstructure were thoroughly investigated, and the treatment effect of microorganism–bentonite combined mineralization method was evaluated. It was found that this method could improve the seepage prevention effect and the stability of sealing of sand, and the permeability coefficient of samples could be reduced by up to 4 orders of magnitude. In addition, the erosion rate during the permeation process was also reduced by several times and reached as low as   0.51 g/(s·m²). Based on the effect of bentonite and calcium carbonate precipitate on sand sealing, the anti-seepage mechanism of microorganism–bentonite combined mineralization method was analyzed. The results show that the microorganism–bentonite combined mineralization method was feasible and efficient in the seepage control of sand, which will provide an important reference for the application of microbial mineralization technology to addressing anti-seepage problems.