The invention discloses a beneficiation method for improving comprehensive recovery indexes of complex low-grade molybdenum polymetallic ores, and particularly relates to comprehensive recovery of valuable elements such as molybdenum, copper and sulfur in low-grade molybdenum ores. According to the method, the effective flotation separation of molybdenite, chalcopyrite and pyrite can be realized,and the comprehensive recovery indexes of the low-grade molybdenum ores are improved. The method comprises the following steps of primary ore grinding, molybdenum (molybdenite) flotation, secondary ore grinding (rough molybdenum copper concentrate regrinding), copper (chalcopyrite) flotation, and sulfur (pyrite) flotation. The method is stable and effective in reagent regime and beneficiation process flow and high in adaptability. By using the beneficiation method, high-quality molybdenite, chalcopyrite and pyrite are obtained from the complex, difficult-to-select and low-grade molybdenum polymetallic ore with associated copper/ sulfur, and the comprehensive recovery indexes of sulfide minerals are excellent. The adopted reagent is non-toxic and harmless, has little influence on the environment, and is an excellent beneficiation method.