Microbial induced calcite precipitation (MICP) can protect the surface of porous cement-based materials and enhance the durability of concrete, the efficiency of which depends on the near surface property. Therefore, this paper is aimed to investigate the effects of bacterial solution to cementation solution ratio (1:2, 1:1 and 2:1) and different calcium sources (calcium chloride, calcium nitrate and calcium acetate) on compressive strength and capillary water absorption coefficient of MICP-treated mortar, and attempted to establish the relationship between microstructure and macroscopic property. The results indicated that the surface treatment by MICP significantly reduced the capillary water absorption coefficient, while it slightly affected the compressive strength of mortar. Supplying calcium source of calcium chloride or calcium nitrate, setting bacterial solution to cementation solution volume ratio of 1:1 were beneficial to improve the compressive strength and reduce the coefficient, in which the CH content of the near surface layer was reduced and the calcite content of that was increased, it showed limited influence on the hydration products of the interior substances. Nanoscale calcite generated in the near surface layer consumed the CH and filled in gel pores to increase the Ca/Si ratio of C–S–H. The increased compressive strength was due to the refined pore structure of the near surface layer, in which the combination effect of improved pore structure of the near surface layer and the precipitation layer of MICP on the surface effectively reduced the coefficients.