Paddy water management for saving water, maintaining high rice yield, reducing pollution and fertilizer maintenance has a great significance for the agriculture development in China. The aim of this study was to evaluate water level management schemes in all growth stages for flooding and drought paddy field based on the indicators of the yield, water use efficiency (WUE), the losses of ammonia nitrogen (NH₄⁺-N) and the total phosphorus (TP), and the available nitrogen (RAN) and available phosphorus (RAP) content in soil by using entropy weight TOPSIS model. The results showed that, rice yield, soil RAP and RAN had significant difference for flooding and drought treatments. As for WUE, water supply was favorable for higher WUE in the early growth stage of rice, and moderate drought could improve WUE in the late growth stage. With drought conditions, it could not only reduce water consumption, but also improve water use efficiency and yield. Also, the averaged nonpoint source pollution for drought treatments was higher than that for flooding treatments. Water leakage was crucial for yield production. TOPSIS modeling showed that, for flooding field, leakage intensity should be controlled at 4 mm d^-1, in tillering stage, with flooding time lasting 5 days, and suitable flooding depth was 100 mm; in jointing-booting and milkying stage, flooding time lasted 5 days, and suitable flooding depth was 250 mm; for heading-flowering stage, flooding time lasted 7 days, and suitable flooding depth was 200 mm; for drought paddy field, in tillering stage, drought time lasted 7 days, suitable drought depth was -300 mm; while in the other stages, drought time lasted 5 days, and suitable drought depth was -600mm. With drought condition, NH₄ ⁺-N, NO₃^--N and TP loss was 66.72%, 55.56% and 42.81%, respectively lower than that for flooding treatments.