The invention discloses a method for prefabricating and constructing a separated rail structure. The separated rail structure comprises a separated rail bearing groove and a factory-prefabricated rail system. The method for prefabricating the separated rail structure includes the following steps of preparing materials, controlling temperatures, arranging the rail bearing groove, cleaning a groove area, mounting a tie plate under a rail, placing the steel rail, checking and sealing the end, treating before pouring and pouring polymer materials. The method for constructing the separated rail structure includes the following steps of hoisting a rail bearing groove rail system, conducting foundation treatment, placing the prefabricated rail bearing groove and adjusting the geometry, connecting and fixing, pouring concrete, maintaining and removing tools. According to the method for prefabricating and constructing the separated rail structure, the construction technologies of factory prefabrication, field assembly and the like are used, the fastening-down rail temperature of the rail system is effectively controlled in a factory, the influence of the site construction environment and climate is avoided, the construction cost of the rail is lowered, the efficiency is improved, and maintaining and replacing are more convenient.