The invention provides a method for separating and extracting copper and cobalt-nickel in low-grade complex mixed copper-cobalt ore, which uses low-grade complex mixed copper-cobalt ore (sulfide and oxide) as a raw material to extract an intermediate product of the copper and cobalt-nickel by adopting process flows of crushing and grinding ore into slurry, leaching the slurry with acidic villaumite by a wet method, extracting copper powder by reduction and replacement, vulcanizing and depositing nickel (cobalt), concentrating, drying, baking and hydrolyzing deposited mother solution at low temperature and the like. The method comprises main technical points that metallic elements in the mixed copper-cobalt ore are dissolved and leached by the acidic villaumite under normal pressure; copper in leaching liquor is reduced and deposited by a reducing agent; the cobalt and nickel are deposited by a vulcanizing agent to obtain the intermediate product; the mother solution is concentrated, dried, baked and hydrolyzed at low temperature after cobalt-nickel deposition to obtain metal oxide, metal oxychloride and hydrogen chloride containing iron, magnesium and the like; hydrogen chloride is reclaimed to obtain hydrochloric acid, and baked solid is leached into water to obtain chloride solution; and the hydrochloric acid and the chloride solution are used for leaching of ore slurry. The method comprehensively reclaims the copper, the cobalt-nickel and the like, and has the characteristics of high leaching rate of the copper and the cobalt-nickel, less energy consumption, low cost, closed circulation of chlorine (hydrochloric acid), less investment of project engineering and the like. The whole process is concise, clean and environment-friendly. The method is particularly applicable to large-scale industrial production.