Abstract: Reagents are the core to achieve the separation of copper and molybdenum. NaHS(Na₂S), Knox reagent, sodium thioglycolate and cyanide are commonly used copper molybdenum inhibitors, with the problems of the high dosage, high cost, severe environmental pollution, low industrial applicability and etc. To solve these problems, based on fragment assembly used in study, the method "screening to identify lead compounds, splicing and reassembling the lead compound, with the combination of computer aided molecular design techniques" was conducted to efficient inhibitor BK511. Material Studios (MS) software was used to calculate the interaction between BK511 and chalcopyrite. The results illustrated that the interaction between BK511 and chalcopyrite is significantly greater than that of NaHS and etc, to achieve selective inhibition of chalcopyrite. The industrial application of Cu-Mo separation showed that BK511 displayed outstanding inhibition performance with only 10%~20% dosage of NaHS, which is a solid candidate to substitute NaHS with much lower reagent cost and better environment footprint. The sulfide content is dramatically reduced in the tailings of the processing plant in the industry.