Efficient management of irrigation water, nitrogen fertilizer and planting area of rice is helpful to improve agricultural economic efficiency, resource utilization efficiency and ecological environment. Taking 13 cities (districts) in Heilongjiang Province as the study area, Meta analysis was used to quantify the effects of different irrigation methods and nitrogen application rates on rice yield and greenhouse gas emissions (CO2, CH4, N2O),and the water-fertilizer production function was established. Furthermore, a multi-objective optimization model was established with economic benefit, greenhouse gas emission and water and fertilizer utilization efficiency as objective functions to optimize the allocation of water and fertilizer resources in different regions and adjust the rice planting area. The results showed that controlled irrigation and application of nitrogen fertilizer had different effects on yield and greenhouse gas emissions. After optimization, rice planting area was reduced by 3.76% and water use efficiency was increased by 18.4%, the amount of irrigation was 4513.54m3/hm2. The nitrogen application rate was reduced by 11%, and the nitrogen use efficiency was increased by 32%, the amount of nitrogen fertilizer applied was 100kg/hm2. Economic benefits were increased by 8.1%, and environmental pollution was decreased by 10.6%. The model can quantify the response of controlled irrigation based water and fertilizer application to yield and greenhouse gas emissions at regional-scale, synergistically optimize water-land-fertilizer resource allocation in rice paddies, balance economics, greenhouse gas emissions, and resource efficiency, it was helpful to optimize water and nitrogen resources and adjust planting area between different targets of rice in Heilongjiang Province, so as to promote sustainable agricultural development. It can provide reference for the optimization and management of soil, water and fertilizer resources of rice.