The invention discloses a selective flocculation-column flotation recovery method and system of micro-fine particle molybdenum cleaner tailings. The method includes the following steps that: a dispersing agent and a collecting agent are added, so that first stirring and pulp conditioning is performed, and therefore, mineral particles can be fully dispersed, and the surface hydrophobicity of target mineral particles can be improved; a flocculating agent and a foaming agent are added, so that second stirring and pulp conditioning is performed, and therefore, the target mineral particles can be flocculated selectively; the cyclonic-static fine bubble floatatation column is utilized to perform copper-molybdenum mixed floating, and a roughing-concentration-scavenging floatation process is adopted, and as a result, copper-molybdenum mixed floated concentrates and tailings can be obtained; an inhibitor is added in the copper-molybdenum mixed floated concentrates, so that third stirring and pulp conditioning is performed; and the cyclonic-static fine bubble floatatation column is utilized to perform copper-molybdenum separation, and a roughing-concentration floatation process is adopted, so that molybdenum concentrates and copper concentrates can be obtained. According to the selective flocculation-column flotation recovery method and system of micro-fine particle molybdenum cleaner tailings of the invention adopted, two kinds of micro-fine particle separation ways, namely, selective flocculation and column flotation, are adopted to recover molybdenum and copper in molybdenum concentrates and tailings, and therefore, the comprehensive utilization rate of mineral resources can be improved, and the selective flocculation-column flotation recovery method and system have excellent economic benefits and social benefits.