This dataset presents apparent carbon dioxide emissions totals for 353 prefecture-level cities in China from 1997 to 2020. Compiled based on the 2015 revised edition of energy data from the National Bureau of Statistics of China, the prefecture-level city emissions figures were derived by aggregating emissions from subordinate counties. Units are in million tons. It can be used for analyzing the spatiotemporal characteristics of carbon emissions at the prefecture-level city scale, formulating emission reduction policies, and evaluating low-carbon development. This dataset fills the gap in long-term carbon emission data for prefecture-level cities.