The invention discloses a composite intermediate phase negative electrode material, a lithium ion secondary battery, a preparation method and application. The preparation method comprises the following step: carrying out catalytic graphitization treatment on a blocky mixture containing uncalcined green coke powder, mesocarbon microbead green pellets, a graphitization catalyst and an adhesive capable of being graphitized, wherein the particle size D50 of the uncalcined green coke powder is 1-50 [mu] m, and the mass ratio of the uncalcined green coke powder to the mesocarbon microbead green pellets is (0.25-1): 1. The composite intermediate-phase negative electrode material prepared by the method is large in discharge capacity and good in cycle performance; a prepared button cell has excellent comprehensive performance, the discharge capacity is 365 mAh/g or above, the cycle performance is good (300 cycles, the capacity is maintained to be greater than or equal to 90%), the safety is better (130 DEG C/60 minutes, explosion and expansion are avoided), the adaptability to electrolytes and other additives is better, the preparation method is simple and feasible, and the preparation method is suitable for industrial production.