The invention provides a power generation system for waste heat of medium and low temperature flue gas with cylinder organic medium evaporation, and belongs to the technical field of energy and environment. The invention comprises a heat pipe system, a working medium circulation loop of organic Rankine cycle, a medium and low temperature flue gas exhausting pipeline, a heating hot water loop and a cooling water loop, wherein an ascending pipe and a descending pipe of a boiler are replaced by heat pipes, the flue gas heat exchanger and the boiler cylinder are an integrally cylindrical structure, and is separated to the upper boiler cylinder and the lower flue gas heat exchanger by two layers of insulation partition, the lower end of the heat pipe is arranged in flue gas heat exchanger, the upper end is arranged in the boiler barrel, toluene, dichlorotrifluoroethane, propane and pentafluoropropane are used as working medium, and 20% volume of the softening desalted water is used as the heat pipe working fluid. The invention has advantages of little space occupation, small heat exchange between heat pipe and air, high efficiency of heat exchange, convenient heat pipe replacement, being capable of avoiding the heat exchanger pipe corrosion and the working medium leakage and other advantages, and being capable of adjusting the exhaust regenerative heat of organic Rankine cycle according to the heating load demands.