Aerodynamic loads are an important type of load in finite element analysis of aircraft structures. Due to the mismatch between the mesh used in computational fluid dynamics (CFD) and the one in structural analysis, and the load can be given in the form of a coordinate-pressure table, three-dimensional interpolation of the aerodynamic load input is often required before it can be applied to the structural mesh. A modified radial basis function interpolation method is proposed, where neighboring space of the interpolation point is distorted according to its normal vector, thus reducing the interference of non-coplanar sampling points. Additionally, it enhances the algorithm efficiency by incorporating a KD tree data structure. This modified radial basis function interpolation method can obtain a load spectrum matching the structural mesh based only on the coordinate-pressure table. The feasibility of the method is demonstrated through interpolation of aerodynamic loads for several typical aircraft structures. The results show that the modified radial basis function interpolation method provides an effective means for accurately applying aerodynamic loads in the finite element analysis of aircraft structures, and has important application value.