The invention provides a method and system for recovering main associated elements from copper-nickel sulfide ore. The method comprises the following steps: 1, continuously adding low-grade nickel matte and a leaching reaction solution into a reaction base solution, carrying out selective leaching, and collecting hydrogen sulfide gas, a first leaching solution and a first leaching residue, wherein the leaching reaction liquid is sulfuric acid with the mass fraction being 60-95%; 2, adding water into the first leaching residue for dissolving the first leaching slag, and collecting a second leaching solution and a second leaching residue; and 3, removing iron from the second leaching solution, collecting an iron-removed solution used for extracting nickel and cobalt and an iron-removed residue used for iron making, and / or sending the second leaching residue to a copper smelting device for smelting to obtain copper and noble metal. According to the method, deep separation of the nickel and the copper can be realized, and recovery of the nickel, the copper, the cobalt, the noble metal and sulfur can be effectively realized. The method is simple in process, short in flow and high in efficiency, is a clean and efficient element recovery process and is easy for large-scale industrial production.