The whole flow passage of Francis turbine including clearance structure such as cavity between crown and top cover, weep hole and seal passage of runner was built to study pressure distributions and velocity distributions in main passage as well as clearance flow characteristics by CFD method. Variation rules of leakage flux and static pressure in chamber head of the turbine was revealed due to different micro channel clearance widths, weep hole diameters and numbers. ICEM structured grid was used to divide the key components to analyze the seal clearance flow. The sizes of grid nodes were set up as one smaller regional area and another larger one according to the large space between the main passage and seal passage. The numerical results showed that seal widths, weep hole diameter and number had an impact on flux leakage and pressure in chamber head. According to numerical simulation results, the weep hole number was determined as 6, weep hole diameter was 40mm and seal width was 1mm. Under the rated condition, turbine installation efficiency was 86.75% with flow rate of 5109m3/h, and the clearance leakage reach 0.3% of the whole unit flow. The calculation results agreed well with the test, which showed that clearance flow calculation method could provide scientific basis for the design of Francis hydraulic turbine weep hole diameter and number, and details of seal gap structure. The results would benefit to avoiding the hydraulic vibration and ensure the secure and efficient operation of units.