Pre-planning for a rational survey design is essential to improve the reliability and efficiency of the acoustic assessment of fishery resources in large water bodies. In this study, we compared the differences in acoustic estimates of fish resources between triangular and parallel transect designs in the Three Gorges Reservoir (TGR, China), aiming to provide a reference for fishery acoustic survey planning in such canyon-shaped reservoirs. We conducted hydroacoustic surveys using an echosounder (SIMRAD EY60, 120 kHz) in the Yangtze mainstream near the dam and an adjacent tributary with triangular and parallel designs. The independent samples t-test showed that the acoustic estimates of fish density were not significantly different between these two types of survey designs for both mainstream and tributary. The Fisher’s exact test indicated that there was no significant difference in fish size distributions, as measured by target strength (TS), between survey designs either. In view of reducing time spent in nearshore areas to improve efficiency and ensure safety, we recommend that the triangular design with reliable coverage be given priority for hydroacoustic sampling in the TGR and similar canyon-shaped reservoirs, especially when sampling at night.