The invention provides a factory eggplant double-root-cutting grafting seedling raising method. The method comprises the following steps of debugging equipment, preparing raw materials (inoculating rootstocks, scions and the like), carrying out matrix nutrition proportioning, carrying out germination accelerating treatment, sowing and transplanting, carrying out double-root-cutting grafting, healing, carrying out seedling hardening management, and standard finished products emergence. The production design is ordered, the production period is fixed for 80 days, automatic coordination of factory matching water, temperature, fertilizer and air is realized, high grafting survival rate, difficulty in excessive growth, neat and strong seedlings, consistent cultivation standard and strong seedlings are achieved, vegetable seedling quality is improved, soil harmful disease (eggplant verticillium wilt and bacterial wilt) resistance is remarkable, secondary infection prevention effect after plant formation is good, grafting seedling recovery time is shorter and faster, the survival rate is higher, the growth vigor is stronger, the root system is strong, the stress resistance is strong, the yield is high, the quality is better, and the technology breaks through the defects of the conventional grafting technology; and the grafting process is easy to decompose, suitable for industrialized seedling production and capable of reducing labor intensity.