Understanding of fish community structure is the basis of determining appropriate strategy to control the alga bloom. To regulate fish community structure scientifically and define a rational biomanipulation strategy, hydroacoustic investigation were carried out in Yudong Reservoir with Simrad EY60 split-beam echo sounder in July of 2013, accompanied with the sampling of Nordic multi-mesh gill nets (mesh-size=8.5, 4.0, 12.5, 2.0, 11.0, 1.6, 2.5, 4.8, 3.1, 1.0, 7.5 and 6.0 cm). A total of 12 fish species were collected and the density was 638.4±310.2 ind./1000 m³. Fish distributed unevenly and its density tend to increase from dam part, middle part, tributary part to upper part of the reservoir, with density of 521.5±371.3, 561.9±189.2, 653.7±323.7, 1137.1±90.4 ind./1000 m³, respectively. Moreover, fish in the upper reservoir has a bigger size than that in other parts. The vertical distribution pattern is:97.6% fish habitat in the 0-10 m layer while there was only 2.4% fish distributed in waters deeper than 10 m, average target strength in the 0-20 m layer was highest (-58.6 dB) while the 20-40 m layer was lowest (-63.9 dB). The Multivariate regression tree model indicates that temperature and water depth have significant impact on fish density. To control the algae bloom, we suggest to enhance stocking of Silver Carp and Bighead Carp, and to introduce endemic piscivorous fishes at the same time to regulate fish community.