This study compared the effects of four different tilapia cultivation systems (a tilapia-water spinach integrated system, a sewage discharging system, a sewage discharging and tilapia-water spinach integrated system, and a tilapia monoculture system as a control) on the variations in water quality, tilapia production, and off-flavor contents in water and tilapia in June, July, and August 2016. Using gas chromatography and mass spectrometry (GC-MS) based on microwave-assisted distillation followed by purge-and-trap, the off-flavor compounds geosmin (GSM) and 2-methylisoborneol (2-MIB) were determined in water and tilapia tissue. The results showed that production in the tilapia-water spinach integrated system was the highest among the systems examined (<0.05). The contents of ammonia nitrogen and nitrite in the sewage discharging and tilapia-water spinach integrated system were significantly lower compared with the control group[(0.67±0.02) μg/kg and (0.870±0.018) μg/kg]. In addition, the concentrations of 2-MIB and GSM in the muscle of tilapia in the sewage discharging and tilapia-water spinach integrated system[(0.31±0.02) μg/kg and (0.53±0.042) μg/kg] were significantly lower than those in the control group[(0.67±0.02) μg/kg and (0.870±0.018) μg/kg, respectively]. These results indicate that the sewage discharging and tilapia-water spinach integrated system reduced the accumulation of off-flavor compounds in water and tilapia muscle in an intensive tilapia farming system.