The CO2 atmosphere in the flue gas of cement kiln was simulated in this paper, and different methods were used to activate the RHCP with particle size < 75 µm under normal temperature and pressure. The effects of different activation methods were studied, and the mechanism of CO2 storage was clarified. On the basis of concrete carbonization curing, a new technology based on MICP was proposed. During the activation of RHCP, a Bacillus strain capable of secreting carbonic anhydrase was introduced into the CO2 carbonization system of RHCP. Carbonic anhydrase could accelerate the capture and conversion of CO2 into bicarbonate ions and carbonate ions. Calcite-type CaCO3 and amorphous silica gel were formed by the reaction of CO2 with active components in RHCP. Finally, the generated product filled the pores to make the microstructure of the slurry denser, and CO2 was also permanently sealed. The results showed that the MM-RHCP not only improved the activity index of the mortar, but also improved the potential for storing CO2 in RHCP. Through FT-IR, XRD, SEM-EDS, TGA and nitrogen adsorption pore size analysis, it was further proved that the use of microbial mineralized RHCP could accelerate the formation of CaCO3, ettringite and SiO2·n H2O. In addition, the CO2 storage capacity of MM-RHCP was greater than that of DC-RHCP and LP-RHCP. The RHCP after mineralization treatment could replace cement as mineral admixture, and this technology realized the resource utilization of solid waste. At the same time, CO2 was permanently fixed in RHCP. Therefore, it provided a new way for deep carbon sequestration in the cement industry.