To explore the effects of ETS microbial fertilizer on water quality and yield of rice and crab of rice-cum-crab paddy fields, ETS microbial fertilizer was applied to paddy field and compared with ordinary farmyard manure fertilizers in a test. In the test, 6 square cells of 100 square meters each were set up, and control group and experimental group were designed with each including three parallels. Each experimental group was applied with ETS microbial fertilizer at 26kg and stocked with 50 young crabs; each control group was applied with Jinzhengda organic fertilizer and slow-release fertilizer at 17.3 kg and stocked with 50 young crabs. Samples were taken and analyzed for determining water quality and the yield of rice and crab. The results showed that: the contents of pH and total phosphorus in the water of experimental paddy field were slightly lower than those of the control group, but the difference was not significant (P>0.05); the contents of nitrite, ammonia nitrogen and nitrate in the experimental paddy field were significantly lower than those of the control group (P<0.05). The rice yield of the experiment group was (1.01±0.06) kg/m2, which was significantly higher than that of the control group (P < 0.05). The average size of the crab (121.3±5.7g) and the crab yield (40.26±0.31 g/m2) of the test group were significantly better than those of the control group (P<0.05). The study shows that ETS microbial fertilizer, when used in paddy field, can reduce the ammonia nitrogen, nitrite, nitrate and other chemical indicators of the water, and improve the yield of rice and crab.