The invention provides a method for biological comprehensive recovery of copper, cobalt and magnesium from copper cobalt sulfide ore containing magnesium. The method comprises the following steps: 1) carrying out acid leaching pretreatment and beginning recovery of magnesium when the concentration of magnesium ions in a pre-leaching solution is 30 g/L or above; 2) carrying out biological dump leaching by using a mixed strain of Thiobacillus ferrooxidans Retech V and Sulfobacillus thermosulfidooxidans Retech-MTC-1; 3) subjecting a pre-leached solution or biological leachate to extraction with a copper extractant and successively carrying out reverse extraction with sulfuric acid and electrodeposition so as to eventually obtain cathode copper; 4) subjecting raffinade obtained after copper extraction to precipitation with limestone so as to remove iron, then carrying out washing, extracting cobalt by using a mixed extractant composed of P507 and cyanax272 and successively carrying out reverse extraction with sulfuric acid and concentration so as to obtain a cobalt salt; and 5) adjusting the pH value of raffinade obtained after cobalt extraction with sodium hydroxide and carrying out precipitation so as to obtain magnesium hydroxide.