China is striving to reach a peak in its carbon dioxide emissions by 2030 and achieve carbon neutrality by 2060. The accurate accounting of carbon emissions is important for achieving these dual carbon goals. An extensive literature review and field measurements were conducted to investigate the specific impact of population density on carbon emissions in large integrated healthcare organizations. This research uses VOSviewer to visualize the literature analysis. We determined that the flow of people is a key factor affecting carbon emissions during the operational phase of large-scale comprehensive medical institutions. Through field measurements, the relationship between the density of pedestrian flow and indoor environment measurements was derived, and the incremental equipment operating loads caused by changes in the indoor environment were analyzed. Using the carbon emission factor method advocated by the IPCC, a carbon emission accounting model based on different flow intervals was constructed, and the energy consumption of different equipment was fully considered according to its proportion. The validation results showed that the error between the calculated value and the actual values of the model was 3.07% (less than 5%), which has good validity. The model calculates the direct and indirect carbon emissions in the operational phase based on the population flow perspective, which can provide a reference for the energy-saving design and green operation of large-scale comprehensive medical institutions. The research will continue to focus on the population flow, and the accounting model will be further optimized through machine learning algorithms.