Reducing soil nitrogen leaching losses and improving nitrogen-use efficiency with effective fertilization management strategies are extremely important for sustainable agricultural development. A 2-year field study was executed with the same nitrogen input in a subtropical rice production system in Southeast China, using chemical fertilizers as a control (CK), to study the influences of different application amounts of Chinese milk vetch (CMV), i.e., 15,000 kg hm−2 (CL), 30,000 kg hm−2 (CM), and 45,000 kg hm−2 (CH), on soil soluble nitrogen stock and leaching risks in a clay paddy field. The results showed that the soil stocks of soluble inorganic nitrogen (SIN) and soluble organic nitrogen (SON) in a 0–60 cm soil profile under different application amounts of CMV significantly increased by 12.43–36.03% and 19.43–71.75% compared with CK, respectively, which was more favorable to soil SON accumulation. In the 2-year experiment, the total dissolved nitrogen leaching loss was 23.51–61.88 kg hm−2 under different application rates of CMV, of which 50.08–62.69% was leached by dissolved inorganic nitrogen (DIN), and 37.31–49.92% was leached by dissolved organic nitrogen (DON). CMV application improved soil properties (pH, SOM, and urease/protease), increased SIN and SON stocks, and decreased surface water DIN and DON concentrations, thereby reducing DIN and DON leaching. The leachings of DIN and DON in different application rates of CMV were reduced by 11.37–66.23% and 13.39–52.07% compared with the CK treatment, respectively. Conclusively, nitrogen leaching loss in paddy fields was severe, and the DIN and DON leaching loss in CMV treatments were lower than those in the control under the same nitrogen input. Thus, replacing nitrogen fertilizer with CMV under the same nitrogen input could reduce the risk of nitrogen nonpoint pollution in clay paddy fields.