The biomanipulation technique has been developed and implemented for decades, yielding favorable results in various lakes both domestically and globally. This technology uses fish to reduce algae biomass, giving a natural and environmentally friendly solution to improve water quality. The effectiveness of biomanipulation technology in large-scale artificial water canals, on the other hand, has been unclear. To address this, from 15 December 2019 to 30 April 2020, an in situ experimental study on the biomanipulation of periphytic algae was conducted in the Lushan section of the main canal of the Middle Route of the South-to-North Water Diversion Project (MSNWDP). The study aimed to verify the control effect of fish on periphytic algae. Various combinations of Megalobrama terminalis and Xenocypris davidi were fixed on the canal with a triangular cylindrical cage, and their feeding effects on periphytic algae were observed. The results showed that the density of periphytic algae at the bottom of the cages was substantially lower than before the experiment, with a 68.75% average reduction. We graded the food-filling results based on the amount of digestive tract content, which was represented using Arabic numerals ranging from 0 to 5. The study discovered that M. terminalis had the best adaptability to the environment, with full intestines primarily composed of periphytic algae and a food-filling degree between grades 4 and 5. X. davidi, on the other hand, had a food-filling degree of 0. Furthermore, the weight of each M. terminalis increased significantly following the experiment, whereas the weight of each X. davidi decreased to varying degrees. Additionally, the study highlights the importance of selecting the appropriate fish species for biomanipulation, as different species may have varying levels of effectiveness in controlling periphytic algae. Overall, this study provides valuable insights into the potential of biomanipulation technology in large-scale artificial water canals and other water conservancy projects.