The invention discloses a method of embedding lithium for a lithium ion capacitor by using third electrodes and belongs to the technical field of manufacture of lithium ion capacitors. A negative pole, a diaphragm and a positive pole diaphragm are cascaded or wound in sequence into each cell and are fixedly assembled with an adhesive tape into the cell; the positive pole and negative pole tabs of three cells are welded respectively together and are then welded in parallel, and lithium-bearing third electrodes are manufactured and are inserted between the sides of the cells; lithium salt containing organic solution is injected from an injection port; a charge-discharge tester is connected for charging and discharging so as to embed lithium in the anode; the third electrodes are removed, and the lithium ion capacitor is manufactured by sealing and suction-packaging. The problem of long lithium embedding term can be effectively solved, the negative pole lithium embedding process is controllable, cycling of the capacitor is facilitated, manufacture cost is low, safety of production process can be improved, other electrode products are not introduced when lithium is added to the negative pole, the technical flow is simplified, and the method is suitable for industrial production.