Taking Chinese Customs statistics from 2003 to 2012 as a sample, this paper makes an empirical research on the structure and dynamic changes of Sino-Russian ecological footprint in trade during this period on the basis of the research on the sustainable development of Sino-Russian trade through the method of ecological footprint calculation. The results show that the bilateral trade between China and Russia are strongly complementary. The ecological footprint in Sino-Russian trade is manifested in China’s main exports to Russia: cultivated land, water area and forest land and China’s main imports from Russia: forest land, water area and fossil fuel. In Sino-Russian trade, China has been in the trade surplus state for a long time. Sino-Russian trade makes China indirectly use the productive land area of Russia, easing the contradiction between the rapid development of China’s economy and the shortage of ecological resources, which is conducive to promoting the sustainable development of China’s economy. Therefore, China should further deepen economic and trade cooperation with Russia and optimize the structure of import and export in order to achieve mutually win-win benefit.