Due to the complexity of axial-flow hydraulic machinery structure and the difficulty of flow field analysis, this paper takes three-dimensional hydrofoil as the research object to analyse the flow characteristics of clearance flow and carry out research on clearance leakage control. The 3-D hydrofoil model with two kinds of gap widths was calculated by using the numerical model method, and compared with the experiment; the influence law of different groove depth and width on the gap leakage flow characteristics and energy characteristics was studied. The results show that with the increase of groove depth, the clearance leakage increases, the lift-drag ratio decreases, and the pressure coefficient increases. Higher axial velocity is shown with increasing groove depth under the small tip clearance, while the opposite is true for large gaps. The optimal groove depth is determined to be D=1mm. When the groove width is 2mm, the pressure coefficient of the hydrofoil is the highest and the vorticity coefficient is the smallest, so the hydrofoil has better performance. In summary, when groove depth D=1mm and groove width W=2mm, the clearance leakage flow rate is smaller and the lift-drag ratio is higher. This study provides a new method for improving the flow field and running stability of turbine-machines with tip clearance in practical engineering.