In order to improve the stable operation efficiency of Francis turbine, the existing Francis runner of a power station was taken as the research object, and based on its prototype structure, the modification scheme of adding a baffle structure between the runner blades was proposed. Based on CFX numerical simulation software and shear stress transport(SST) turbulence model, three-dimensional full-flow channel numerical simulation was carried out for five design conditions, namely 0.3Q_d, 0.5Q_d, 0.6Q_d, 0.8Q_d and Q_d (Q_dis the design flow rate), for the Francis turbine of the two types of structures was systematically analyzed the influence of the baffle structure on the internal flow field of the runner, the flow characteristics of the blade surfaces, and the draft tube flow pattern. The results show that the baffle structure has a significant effect on the flow characteristics of the turbine under various operating conditions, and the efficiency of the turbine with an additional baffle structure is higher than that of the prototype turbine under various operating conditions. Among them, the optimised runner efficiency reaches 93.8% at Q_d, which is 0.6% higher than the prototype. The efficiency improvement is more significant at low operating conditions, and the optimised runner efficiency is 54% at 0.3Qd, which is 6% higher than the prototype. After adding the baffle, the flow lines on the surface of the runner blades and in the draft tube tend to be smoother, and the vortex and flow turbulence are reduced, which significantly improves the flow pattern of the runner and the draft tube. At the same time, the distribution of physical quantities inside the runner is more uniform, and the fluctuation range is reduced. The runner shows better adaptability to multiple operating conditions, and the research results provide important theoretical reference and engineering basis for the optimisation of the runner of the Francis turbine.