A field trail was conducted to evaluate the effects of conventional cultivation and rice-frog co-cultivation on the physicochemical characteristics and dynamic changes of nutrients of the soil and grain yield. The results showed that compared with CK, rice-frog co-culture increased the pH, electrical conductivity, total phosphorus and available phosphorus content of the soil, but decreased soil total nitrogen, alkali hydrolyzable nitrogen, available potassium, and organic matter content of the soil. During the same growth stage of rice, the soil nutrient content of DWH treatment (rice-frog co-culture with higher density frog) was higher than DWL treatment (rice-frog co-culture with low density frog). DWL treatment decreased rice yields significantly by 12.0%, while DWH treatment decreased rice yields by 3.1% with no significant difference compared with CK. The main reason for the decrease in rice yield caused by rice-frog co-culture was that it significantly reduced the effective panicle number of rice. It can be seen that cultivating an appropriate number of black spotted frogs under a rice cropping system will lead to a small decrease in rice yield, but improve the safety of rice and the output of black spotted frogs. Not only does it help to increase the economic benefits of rice fields per unit area, but also reduces environmental pollution and achieves better ecological benefits because the absence of chemical fertilizers and pesticides during production.