Much attention is being given to estimating cement-related CO2 emissions in China. However, scant explicit and systematical exploration is being done on regional and national CO2 emission volumes. The aim of this work is therefore to provide an improved bottom-up spatial-integration system, relevant to CO2 emissions at factory level, to allow a more accurate estimation of the CO2 emissions from cement production. Based on this system, the sampling data of cement production lines were integrated as regional- and national-level information. The integration results showed that each ton of clinker produced 883 kg CO2, of which the process, fuel, and electricity emissions accounted for 58.70%, 35.97%, and 5.33%, respectively. The volume of CO2 emissions from clinker and cement production reached 1202 Mt and 1284 Mt, respectively, in 2013. A discrepancy was identified between the clinker emission factors relevant to the two main production processes (i.e., the new suspension preheating and pre-calcining kiln (NSP) and the vertical shaft kiln (VSK)), probably relevant to the energy efficiency of the two technologies. An analysis of the spatial characteristics indicated that the spatial distribution of the clinker emission factors mainly corresponded to that of the NSP process. The discrepancy of spatial pattern largely complied with the economic and population distribution pattern of China. The study could fill the knowledge gaps and provide role players with a useful spatial integration system that should facilitate the accurate estimation of carbon and corresponding regional mitigation strategies in China.