Agricultural intensification has led to the use of high inputs of chemical fertilizers into rice-cultivated lands, and nitrogen and heavy metals in runoff loss from land were a major environmental problem. It is important to mitigate nitrogen and heavy metal pollution for the water body. The nitrogen and heavy metal transformation in the rice field surface water was studied by applied combined organic and inorganic nitrogen fertilizer plus the nitrification inhibitor 3,4-dimethylpyrazole phosphate (DMPP) in the sandy loam paddy soil and blue clayey paddy soil. The results showed that, the application of DMPP in the rice field in organic and inorganic fertilizer combined application models decreased the heavy metal average concentration of total Cu, Zn, and Cd by 22.1 to 30.2, 33.1 to 36.9, and 10.9 to 17.5% in surface water, respectively. Furthermore, in the sandy loam paddy soil and blue clayey paddy soil, the nitrate, nitrite, and total inorganic nitrogen concentrations decreased by 44.4 and 59.6, 90.3 and 88.6, and 14.2 and 25.4% in the rice field surface water with the DMPP addition, in the organic and inorganic fertilizer combined application models in the rice field, respectively. DMPP could be used as an effective nitrification inhibitor to decline the potential nitrogen and heavy metals runoff loss in the combined application models of organic and inorganic fertilizers in some rice fields, minimizing the nitrogen and heavy metal transformation risk from agricultural fields to the water body and being beneficial for protecting the ecological environment.