To obtain the flow mechanism of the transient characteristics of a Kaplan turbine, a three-dimensional (3-D) unsteady, incompressible flow simulation during load rejection was conducted using a computational fluid dynamics (CFD) method in this paper. The dynamic mesh and re-meshing methods were performed to simulate the closing process of the guide vanes and runner blades. The evolution of inner flow patterns and varying regularities of some parameters, such as the runner rotation speed, unit flow rate, unit torque, axial force, and static pressure of the monitored points were revealed, and the results were consistent with the experimental data. During the load rejection process, the guide vane closing behavior played a decisive role in changing the external characteristics and inner flow configurations. In this paper, the runner blades underwent a linear needle closure law and guide vanes operated according to a stage-closing law of "first fast, then slow," where the inflection point was t = 2.3 s. At the segment point of the guide vane closing curve, a water hammer occurs between guide vanes and a large quantity of vortices emerged in the runner and the draft tube. The pressure at the measurement points changes dramatically and the axial thrust rises sharply, marking a unique time in the transient process. Thus, the quality of a transient process could be effectively improved by properly setting the location of segmented point. This study conducted a dynamic simulation of co-adjustment of the guide vanes and the blades, and the results could be used in fault diagnosis of transient operations at hydropower plants.