The present disclosure discloses a method for preparing a citrus-derived complex prebiotic agent. The method comprises the following steps: removing external citrus peels after blanching citrus fruits with hot water, soaking citrus segments after splitting with an acid solution and an alkali solution to remove membranes of the citrus segments, and adjusting the pH of the obtained alkali soaking water with acid soaking water or acid to be weakly acidic or neutral to obtain the complex prebiotic agent, which has the function of reversing intestinal flora disorders. Compared with the traditional prebiotic product preparing method, the product prepared by the method contains prebiotic functional components with different targets such as pectin, flavonoids, oligosaccharides, and other fibers at the same time, and has the efficacies of regulating intestinal flora and reversing intestinal flora disorders caused by antibiotics. At the same time, the preparing method has the characteristics of simple operation and low cost, perfectly supplements a comprehensive utilization process of citrus fruit processing, solves the discharge problem of citrus fruit processing water, and generates very good social benefits.