Ecological compensation is a public policy tool that can be used to cope with excessive fertilizer application and agricultural non-point source pollution; the amount of compensation significantly influences the actual level of policy implementation. This study examined government compensation for a reduction in the amount of fertilizer applied by rice farmers in Nanjing. We used cost income, energy value analysis, and double-boundary contingent valuation methods and constructed a fertilizer reduction compensation standard using the dual perspectives of the government and the farmers.. The results showed that from the perspective of environmental cost quantification resulting from chemical fertilizer pollution, the reference value for application of pure fertilizer to rice cropping systems in Nanjing is 268.75 kg hm^-2 a^-1, which is still approximately 14% lower than the actual amount of fertilizer applied 312.48 kg hm^-2 a^-1 in 2017 in Nanjing. The vast majority of growers were willing to reduce the amount of fertilizer to the reference dosage on the premise of accepting an ecological average compensation standard of 882.49 yuan hm^-2 a^-1. Finally, rice growers with higher education, larger households, and higher fertilizer input costs tended to accept ecological compensation as well as related obligations, whereas older male farmers and those with larger planting areas tended to be more cautious about reducing fertilizer use. Our results provide theoretical support for the prevention and control of agricultural non-point source pollution in Nanjing and the formulation of an ecological compensation standard for paddy fields. In the actual compensation and distribution process, the single compensation standard cannot guarantee fairness and justice and it is necessary to establish a hierarchical ecological compensation system that is linked to the crop planting type and the effects of chemical fertilizer reduction. Farmers should reduce the input of chemical fertilizer as much as possible.