Defects on cement based materials surface can be repaired by using agar as the carrier of bacterial strain. The matching parameters of embedded quantity and carrier content of immobilized bacterial strain and repairing and brushing solution viscosity as well as concentration of immobilized urea/Ca2+ were optimized. The microscale Ca2+ at the defects on the surface of test specimen by adopting acetic acid smear method was disassociated to enhance the cementing power between calcite layer and surface of hardened cement paste with the result that the 100μm thick calcite layer can be mineralized and deposited in situ on the surface of hardened cement paste within three days. The gross absorption coefficient of the repaired hardened cement paste test specimen reduced by more than 90% compared to that before reparation.