Long term operation of hydroelectric units in low load conditions can induce large-scale blade vortices, swirling vortex ropes in the draft tube, and low-frequency high amplitude pressure fluctuation. These phenomena will cause adverse consequences such as excessive vibration of the unit and blade breakage of the runner. Taking inspiration from the protuberances of the leading edge of a humped whale flipper, the present study firstly proposes bionic modifications of guide vanes and draft tube to suppress high-amplitude pressure fluctuations for Francis turbine. Numerical simulations of transient flow characteristics of the prototype unit (PU), the bionic guide vane unit (BG), and the bionic draft tube unit (BDG) under two low load conditions are conducted. Results indicated that the bionic draft tube has a good effect on suppressing pressure fluctuations in the vaneless area and draft tube. Under the Q/QBEF = 0.41 working condition, BDG causes the main frequency amplitude of pressure fluctuation at the center point of the draft tube inlet to change from 8000.2 Pa to 390.9 Pa, a decrease of 95.11 %. Under the Q/QBEF = 0.57 working condition, BDG causes the maximum decrease rate of the main frequency amplitude in the draft tube to be 60.5 %. The reducing effect in BDG of monitoring points in the guide vane area has reached over 43 %. Under low load conditions, the vortices near the wall in the draft tube of BDG are intercepted by bionic structures, reducing the vortex scale and helping to prevent the generation of large swirling vortex ropes. The bionic guide vanes have a significant control effect on pressure pulsation in the the guide vane and vaneless regions, although perform poorly in the draft tube.