The invention relates to a new technique for controlling the forming of a third phase in the extraction process of biological leachate of copper sulfide ore, comprising the following steps: (1) measurement of the viscosity of the biological leachate of copper sulfide ore: a flat-open veitch type standard viscometer is adopted to carry out measurement to the viscosity of the leachate so as to control the forming of the third phase in the extraction process by measuring the viscosity of the leachate; (2) the control of the forming of the third phase: the viscosity of the biological leachate is controlled to be less than 0.96Pa question mark s, i.e., the forming of the third phase is controlled; when the viscosity of the leachate is more than 0.96Pa question mark s, treatment needs to be carried out to the leachate, and the treatment method comprises the following steps of standing, settling, taking supernatant, adjusting the pH value to be 1.3 to 1.5, then returning to ore pile and carrying out biological leaching. The technique directly takes the biological leachate containing Cu<2+>, Fe<2+> and Fe<3+>, has short process, simple equipment, little investment, low cost, no pollution and high recovery rate, and can lead the third phase occurring in the biological leaching of low-grade secondary copper sulfide ore resources to be effectively controlled, thus expanding the utilizing range of resources and improving the recovery rate of the copper metal.