In order to promote the development of new power systems and the consumption of clean energy, pumped storage hydropower stations tend to become increasingly larger in capacity and higher in head height. In this paper, a three-dimensional model of the full channel of a high-head pump turbine is established, and the influence of the gap thickness between the runner crown and the headcover on the internal flow field characteristics, pressure fluctuation characteristics and axial water thrust are studied by means of computational fluid dynamics (CFD). The results indicate that the area where the pressure and velocity vary greatly in the flow field of the crown clearance is at the seal of the labyrinth ring. In addition, the pressure balance pipe has a greater impact on the pressure and flow rate of the water passing through the clearance, and the crown clearance near the pressure balance pipe generates a vortex, resulting in energy loss. Decreasing the thickness of the clearance has no obvious effect on the pressure on the flow-passing components, and increasing the thickness of the clearance has a great change in the pressure values at the upper crown inlet, in front of the labyrinth ring of the crown and in front of the labyrinth ring of the band. The upper part of the vaneless area, the crown inlet and the lower ring inlet are close to the runner; hence, the interference from the rotating parts is the strongest. The effect of increasing the thickness of the crown clearance on the axial water thrust is greater than that of decreasing the thickness of the crown clearance. The pulsation frequency of the axial thrust on the crown, band and blade and the resultant force of the axial thrust increase with the increase in the crown clearance thickness.