The decline in the total fertility rate (TFR) is a key driver of population change and has important implications for population health and social development. However, China’s TFR has been a considerable controversy due to a lack of high-quality data. Therefore, this study used the 2020 national population census of China (NPCC) data and reverse survival method to reassess temporal trends in the TFRs and to reexamine rural–urban differences and regional variations in TFRs from 2000 to 2020 in China. Overall, there were significant gaps between the estimated and reported TFRs before 2020, and the estimated TFRs based on the 2020 NPCC data remained higher than the reported TFRs from government statistics. Although TFRs rebounded shortly in the years after the two-child policy, they have shown a wavelike decline since 2010. Additionally, the estimated TFRs fluctuated below 1.5 children per woman in urban areas compared to above 1.8 in rural areas, but the rural–urban differences continued to decrease. Regarding geographic regional variations, the estimated TFRs in all regions displayed a declining trend during 2010–2020, especially in rural areas. Large decreases of over 25% in TFRs occurred in the north, east, central, and northwest regions. In addition to changing the birth policy, the government and society should adopt comprehensive strategies, including reducing the costs of marriage, childbearing, and child education, as well as promoting work-family balance, to encourage and increase fertility levels.