The invention discloses a collaborative protective mining method for multi-level water resources in a mining area, and relates to the technical field of coal mining. The method comprises the steps that through analyzing layer/division characteristics of a structure of mining overburden strata, the characteristics of a mining-induced stress path in each structural layer and the layer/division characteristics of the permeability of the mining overburden strata, the layer, height, permeability and other parameters of an overburden strata seepage isolation layer are determined; based on an overburden strata ''seepage isolation'' control principle, a mining and separation control effect of the mining parameters and a mining layout method on the multi-level water resources, the collaborative protective mining method for multi-level water resources in the mining area, and a diversion regulating effect are studied, non-destructive monitoring and dynamic evaluation and prediction of water seepage in the surrounding rock at the mining face, the development of cracks in the mining overburden strata, and the change of shallow water level are carried out; and finally a collaborative protectivesystem for multi-level water resources of water blocking of the overburden strata seepage isolation layer, a seepage zone and leakage zone diversion, and collecting water storage of a mined-out area is formed. According to the method, the protection requirements of water amount, ecological water level and water circulation system in an ecologically fragile mining area can be well met, and the application range is wide.