The invention relates to the biotechnical field, and concretely relates to a method for controlling Fritillaria taipaiensis tissue culture endophyte pollution. The control method comprises the following steps: S1, selecting and preprocessing explants: selecting fresh bulbs of Fritillaria taipaiensis, soaking the selected fresh bulbs in a washing powder solution, wiping and flushing the soaked fresh bulbs, and draining the flushed fresh bulbs with filter paper to obtain drained fresh bulbs for later use; S2, disinfecting the explants: soaking the preprocessed explants in a mercury chloride solution, stirring the preprocessed explants and the mercury chloride solution, and rinsing and drying the preprocessed explants on an ultraclean workbench to obtain dried preprocessed explants for later use; S3, carrying out induced differentiation on the small bulbs: breaking the explant bulbs obtained in step S2, longitudinally cutting the broken bulbs to form small dices with the width of 2-4 mm, inoculating a medium containing penicillin and carbendazim with the small dices, and culturing the small dices; S4, subculturing: subculturing the small dices once every 20 days; and S5, carrying out proliferation culture on the small bulbs: transferring the healthy small bulbs obtained in step S4 to a medium containing no bactericidal agents, and culturing the small bulbs. The endophyte pollution control rate of the method for controlling Fritillaria taipaiensis tissue culture endophyte pollution can reach 96.5%.