Clean and deep separation of molybdenum (Mo) and rhenium (Re) from the industrial solutions with ultra-low concentrations are extremely difficult. In current study, various low concentrations of Mo and Re are efficiently separated from the industrial solutions, including lixiviums, eluents and the waste waters, via vapidly stepwise selective coagulation and flocculation precipitation. In-situ generated metal hydroxyl coagulants in the solution have selective coagulation of series isopolymolybdates, while the cetyl-trimethyl-ammonium-bromide (CTAB) has a strong combination with rhenate. The effects of metal ion types, dosages, pH value, and reaction time on the separation behaviors of Mo and Re from the solution are systematically investigated via thermodynamic calculations, SEM-EDS, FT-IR and XPS analyses. It’s found that all the in-situ generated metal hydroxyl coagulants of Cu(II), Al(III), Fe(II) and Fe(III) have selective coagulation of Mo while the Fe(III) hydroxyl coagulant (FeHC) shows the best adsorption performance. After selective coagulation by FeHC, 99.9%Mo is separated while 95.8%Re is kept in the raffinate after filtration. Then the 98.9%Re is further recovered by CTAB flocculation precipitation. The selective coagulation mechanism of Mo and Re by the FeHC is discussed. In addition, this novel technology is applicative for the deep separation of Mo and Re from various low-concentration Mo,Re-bearing industrial solutions.