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This paper studied the effects of tillage, crop residues, and green manure on soil carbon pools and hydrolytic enzyme activity in a sandy loam after five cycles of the rice-wheat system (RWS). Four main plot rice treatments included (1) puddled transplanted rice (PTR) with no wheat straw, (2) PTR with 25% wheat stubbles (12–15 cm long) retained, (3) PTR with no wheat straw plus GM, and (4) PTR with 25% wheat stubbles plus GM. Three subplots treatments in wheat were (1) conventional tillage with rice straw removed, (2) zero tillage (ZT) with rice straw removed, and (3) ZT with 100% rice straw retained as a surface mulch. The results showed that PTR with wheat stubbles retained plus GM and ZT wheat with rice straw retained (ZTWRS100) significantly increased all the carbon pools and hydrolytic enzymes except phenol oxidase and peroxidase activities.