The invention discloses a preparation method of a topological insulator Bi2Se3/FeSe2 alloplasmic structure thin film. The preparation method includes the main steps that a, a FeSe base film is prepared, wherein the FeSe base film is formed on a base sheet through magnetron sputtering; b, FeSe2 annealing phase forming is carried out, wherein the base sheet obtained in the step a and selenium particles are sealed into a vacuum quartz tube with the air pressure smaller than 1*10<-2> Pa, annealing phase forming treatment is carried out, and an FeSe2 thin film is obtained on the base sheet; c, a Bi2Se3 base film is prepared, wherein on the base sheet obtained in the step b, magnetron sputtering is carried out to form a Bi2Se3 film, and then a Bi2Se3/FeSe2 base film is formed on the base sheet; and d, Bi2Se3 annealing phase forming is carried out, wherein the base sheet obtained in the step c and selenium particles are sealed into a vacuum quartz tube with the air pressure small than 1*10<-2> Pa, annealing phase forming treatment is carried out, and the product is obtained. According to the method, the film coating amount is easily controlled, the formed alloplasmic structure thin film is smooth and good in performance. The preparing cost is low.