Although the issue of embodied pollutants in China's supply chains has garnered increasing attention, the dynamic changes occurring within them are unclear. Several existing studies analyse one-year or short-term data in supply chain; however, conducting long-term analyses can yield a deeper understanding of the dynamic changes across the entire supply chain—from production to consumption. This study uses the environmentally extended input–output analysis (EEIOA) and structural path analysis (SPA) methods to investigate the dynamic variation of China’s embodied CH4 emissions in 20 economic sectors from 2000 to 2020, aiming to determine the key supply chain and key sectors. The results reveal that from the final demand perspective, the sector with the highest embodied CH4 emissions has changed from “Agriculture” in 2000 to “Construction” in 2010 to “Other service and activities’ in 2020. The top listed supply chain path of embodied CH4 emissions has also evolved (starting from production to consumption) from “Agriculture→Rural consumption” in 2000 to “Agriculture→Food and tobacco→Urban consumption” in 2010 to “Agriculture→ Urban consumption” in 2020. Notably, the high ranked path, “Agriculture→Food and tobacco→Rural consumption”, shows that the embodied CH4 emission flowing between agriculture and the food industry cannot be ignored. The supply chain path “Coal Mining→Nonmetal Mineral Products→Construction→Capital Formation” has risen from the 17th position in 2000 to the 3rd position in 2020. Thus, it is necessary to control CH4 emissions from sectors upstream, which are predominantly influenced by the construction industry, and a coordinated effort between sectors is also required to effectively reduce emissions. This study provides a comprehensive analysis of China's supply chain over the past two decades. In particular, it suggests policy interventions by controlling critical supply chain paths and key sectors associated with embodied CH4 emission, thereby facilitating the coordinated reduction of anthropogenic CH4 emissions.