A three-dimensional model for Francis turbine's whole flow passage is established in this paper. Simulated calculations of fixed guide vanes, guide vanes, runner and internal flow field of a draft tube are conducted. Velocity vector distribution and static pressure distribution of volute, guide vanes, runner and in the draft tube of the Francis turbine under three operating conditions (design operating conditions, maximum flow conditions, minimum flow conditions) are obtained. Meanwhile, the interblade vortexes in fixed guide vanes, guide vanes and between runner blades of the turbine are compared and analyzed in detail on different operating conditions and at different moments of the same cycle. Therefore, the interblade vortexes in the guide vanes and runner, and the pressure pulsation in the draft tube, as well as its law, especially the inter-relationship between flow separation vortex and its pulsation frequency at the outlet side of the blade under different operating conditions are found out. This is of great guiding significance in improving the operational stability of the turbine.