The invention provides a reservoir optimization scheduling decision-making method and device for aquatic community system stability, and the method comprises the steps: 1, determining a research scene, collecting basic data and historical scheduling data of a reservoir group system, and hydrological data and biomass data of a downstream station, and determining an impact factor and a decision variable of a reservoir scheduling behavior; 2, considering interaction among multiple populations, and constructing a random multi-population dynamic model; 3, calculating hydrological variation degree, describing disturbance of hydrological variation on the aquatic community through noise intensity, establishing a'flow-ecology 'relationship, and analyzing the stability of the aquatic community system under the influence of the hydrological variation; 4, identifying the resilience and the resistance of the multi-population system by adopting two ecological indexes, namely steady-state time ST and a variable coefficient CVST at the steady-state time; and 5, comprehensively considering reservoir water supply and power generation targets and ST and CVST ecological targets, optimizing a reservoir operation curve, and obtaining a reservoir optimization scheduling decision.