To explore hydraulic design method and improve optimization type of the bidirectional shaft passage, the design optimization research of inside and outside line and bifurcation segment type of the bidirectional shaft passage was done. Based on the standard k—ε turbulence model and the Reynolds averaged N—S equation, and combined Longshan hydraulic project, the bidirectional shaft tubular pump device was optimized and designed by using CFD software. The hydraulic loss and velocity distribution in different shaft outlet conduit schemes were calculated and compared, and the different segments hydraulic loss distribution of different shaft outlet conduit schemes was revealed. Finally, combined with the model test results, the reliability of the optimization design of bidirectional shaft flow passage was confirmed. Optimization results showed that the shaft bifurcated segment design directly determined the hydraulic loss of the latter part shaft passage. Through adjusting the shaft inner and outer contour lines, the hydraulic loss of the shaft outlet conduit can be effectively reduced, and the tubular pump device hydraulic characteristics were enhanced. The efficiency curve of the optimized scheme was high, the range of the high efficiency area was wider than that of the initial scheme, and the lift curve was also slightly higher than that of the initial scheme. After optimization, the maximum reverse operation efficiency of the shaft tubular pump system was up to 60.5%, which was increased by 3.8 percentage points compared with the prior optimization, and the forward operation efficiency was 72.18%, which was improved by 1.67 percentage points. The highest efficiency of reverse operation and forward operation model test was 57.56% and 72.67%, respectively. The research would provide guidance for design optimization of low head bidirectional tubular pump device.