The invention discloses a method for comprehensively recovering molybdenum-containing polymetallic gold ore resources, which comprises the following steps: firstly, crushing and grinding molybdenum-containing gold ores first, performing floatation on useful metallic elements to obtain bulk concentrate by a complete mixing floatation method, and discarding tailings; secondly, leaching out and recovering gold and silver from the bulk concentrate by CCL carbon paste wet-method gold leaching technology, and using tailings after gold leaching for preferred selection of molybdenum in the next step;thirdly, performing preferred separation and floatation of the molybdenum on the gold leaching tailings to obtain qualified molybdenum concentrate; fourthly, activating molybdenum-selecting tailings,and performing separation and floatation of lead to obtain lead concentrate; fifthly, performing separation and floatation of copper on lead-selecting tailings to obtain copper concentrate; and sixthly, performing floatation of sulfur on copper-selecting tailings to obtain sulfur concentrate, performing filtration and backwater circulation on sulfur-selecting tailings, and applying the sulfur-selecting tailings to the carbon paste wet-method gold leaching technology for recovery of the gold and the silver. The method greatly improves the grade of separated metals. The following products can be obtained by utilization of the method: more than or equal to 95 percent of alloyed gold, more than or equal to 45 percent of the molybdenum concentrate, more than or equal to 40 percent of the lead concentrate and more than or equal to 35 percent of the sulfur concentrate. The tailings after floatation are filtered by a ceramic filter (the moisture content is less than or equal to 15 percent), subjected to dry-type stacking, and used for soil sealing and land rehabilitation in late stage.