Complete and accurate accounting of greenhouse gas (GHG) emissions from coal mines in China is a critical basis for identifying mitigation potential and making reduction strategies. Previous studies based on the emission factor method and life cycle assessment are limited in accounting scope completeness, data reliability, or result applicability at multiple scales and benchmarks. The objective of this study was to carry out a multi-scale multi-benchmark GHG accounting of Chinese coal mines to build a shared understanding and facilitate discussion on this topic. We established a complete accounting model to cover upstream indirect, direct, and downstream indirect GHG emissions related to coal mining. A total of 1151 operating coal mines were investigated to model site-level carbon emissions based on mass and energy benchmarks and then aggregated to 99 cities, 19 provinces, and the country for accounting. The results showed an over 14-fold variation in mass-based site-level accounting, with the highest uncertainty of less than 15%. This variability performed almost the same at city-level aggregating, whereas narrowed to over twofold at the provincial level. Energy-based accounting presented an over 17-fold variation at the site-level with a similar uncertainty to mass-based accounting. Such variability was narrowed to over sevenfold and approximately threefold in the city- and province-level aggregations, respectively. The national average mass- and energy-based carbon footprint of coal mining were 0.39 kg CO2-eq/kg and 0.0185 kg CO2-eq/MJ, respectively, in which approximately 36% of the total GHG emissions were omitted if mining methane escape was reported only. These results suggest improving the methane utilization rate and optimizing coal production and consumption patterns, which implicates cleaner production and sustainable development strategies for the coal industry in China. The conclusions are helpful to identify individual carbon emission gaps, clarify regional emission responsibilities, coordinate the national carbon neutrality process, and promote a low-carbon coal supply system.