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The joint operation of surface water and groundwater is an effective way to solve the shortage of water resources in arid areas of Northwest China, which is of great significance for efficient utilization of water resources. Taking the Heihe River Basin in Gansu Province as an example, this paper proposes two water supply mechanisms: groundwater based, surface water compensation and surface water based, and groundwater compensation. Taking the groundwater withdrawal and surface water reservoir level as optimization variables, a multi-objective model considering irrigation and ecology and considering hydropower generation is established, and Parallel Flower Pollination Algorithm (P-FPA) is introduced to solve the problem. The results show that the water supply mechanism based on groundwater and surface water compensation can significantly improve the downstream ecological objectives on the basis of meeting the irrigation guarantee rate in the middle reaches; the parallel flower pollination algorithm has significant stability and optimization ability, which is a new method for reservoir optimal operation. The research results not only provide a new idea for the joint operation of surface water and groundwater in arid areas, but also provide important guidance for alleviating the water resources contradiction and improving the utilization efficiency of water resources in Heihe River Basin. • This paper proposes two different methods of joint operation compensation for surface water and groundwater. • The parallel flower pollination algorithm has significant stability and optimization ability. • The groundwater-based operation mode with surface water compensation is more in line with comprehensive benefits. [ABSTRACT FROM AUTHOR]