Under partial load operating conditions, vortex rope generation in the draft tube of a Francis turbine is considered one of the main reasons for hydro unit vibration. In this paper, a Francis turbine HLA551-LJ-43 in the laboratory was taken as a prototype. Numerical simulations of the entire flow passage were carried out. Four different hydro-turbines were chosen to analyze the effect of vortex suppression, which were named the prototype turbine (N-J), the turbine with J-grooves installed on its conical section (W-J), the one with extending runner cone (C), and the one that considered the J-grooves and the extending runner cone at the same time (J+C). Under the part load conditions in which the vortex rope is easily generated (0.4–0.8 times design flow QBEP), the spectrum characteristics of pressure fluctuation, the morphology of vortex rope, and the energy dissipation based on the entropy production theory in the draft tube were studied. The results show that the three optimized structures W-J, C, and J+C could reduce the pressure pulsation in the conical section of the draft tube, weaken the eccentricity of the vortex rope, and decrease the energy losses in the runner and draft tube. It is worth mentioning that the turbine with a J+C optimized structure had the most potent effect on vortex suppression and energy dissipation. Primarily when operating in deep partial load (DPL) conditions, the efficiency of the turbine with a J+C optimized structure was increased by 13.7% compared to the prototype turbine, and the main frequency amplitude of the pressure pulsation in the draft tube was reduced to 32% of the prototype.