The rational allocation of resources will promote the continuous forward development of green economy. This paper designs a multi-objective linear programming model based on regional green development efficiency. Considering the comprehensive multi-objective resource allocation scheme to minimize the green resource input and maximize the economic output. The multi-objective particle swarm optimization algorithm (MOPSO) is introduced to explore the non-inferior solution set of regional resource allocation by combining the non-dominated sorting and congestion comparison strategies. The results show that the multi-objective particle swarm optimization algorithm has faster convergence speed and smaller objective function values among the three standard test functions. The algorithm was used to optimize crop water allocation and 180 sets of non-inferior allocation solutions were obtained. Among them, with the increase of water allocation, the net irrigation benefits of three crops increased continuously to 26.37*103 yuan/hm², 30.54*103 yuan/hm², and 18.57*103 yuan/hm².