The anthropogenic heat emitted into the atmosphere has increased significantly in urban areas with accumulated building and increased energy consumption. Carrying out anthropogenic heat flux (AHF) estimation and exploring the correlation between the AHF and building characteristics (density and height) helps reveal the urban climate's genetic mechanism. This study took Shanghai, Nanjing, and Hangzhou, the typical cities in the Yangtze River Delta region of China as case studies. The annual AHF of 2000, 2008, and 2016 based on the energy consumption inventory and multi-source remote sensing data was estimated. Besides, the monthly AHF by time dimension downscaling processing was obtained. The correlation between AHF and building characteristics was then analyzed by combining urban classification and building block data. The results showed that the AHF of typical cities increased significantly from 2000 to 2016, and the difference between the AHF of building area and the whole city was 12.69–20.36 W·m−2. Monthly AHF had a stratification phenomenon in different building characteristics. Moreover, building characteristics' impact on monthly AHF in the winter was more evident than that in the summer. The AHF of the building growth region was higher than that of the non-growth region, and the differences were more significant in the winter months (1.94–2.23 W·m−2) than in summer months (0.59–0.94 W·m−2). Building density on AHF was more significant than building height, and its contribution was higher than 80% on average in typical cities.