Focusing on the influence of pressure fluctuation in draft tubes when small hydropower run at low load, this paper establishes a hydraulic turbine model with pressure fluctuation and uses sine wave superimposed random signal to simulate pressure fluctuation. It analyzes the effect of fluctuation characteristics in draft tubes on small hydropower isolated operation. Through numerical experiments, it’s found that the turbine mechanical power and active power fluctuation amplitude is proportional to pressure fluctuation amplitude. The pressure fluctuation frequency is closer to the inherent generator oscillation frequency, the active power fluctuation amplitude is larger. Based on the analysis, it gives the way to restrain influence of pressure fluctuation in draft tubes and provides guidance for small hydropower operation.