China, the world’s largest soybean importer, started a new trading system in 2002 in an effort to separate the trading of imported genetically modified (GM) beans and domestically produced non-GM (NGM) beans. To date, all published analyses about China’s soybean futures-to-cash relationship have focused on trading footprints before the establishment of this new system. This study examines the short-run and long-run integration within the Chinese soybean futures market under the new trading system. Standard ordinary least squares (OLS) and error-correction models were used to test cointegration. The test results showed that the Chinese NGM soybean futures market is efficient, that futures prices respond effectively to exogenous price shocks and cash prices move following these futures prices. The results provide important price risk management and price discovery implications to participants in China’s soybean industry, government policy planners and international traders, such that the market enables traders and processors to effectively hedge against price risks and help producers make better production decisions.