The invention discloses a method for automatically generating a hexahedral mesh with a boundary layer of a reactor fuel assembly, which comprises the following steps of: 1, performing geometric pretreatment, and reserving a thickness space of a boundary layer mesh on the surface of a fuel rod; 2, partitioning the fluid area, namely partitioning the fluid area into a complex geometric area with stirring and mixing wings and a simple geometric area; 3, utilizing a tetrahedral mesh division method to complete mesh division of the complex geometric area with the mixing wings obtained in the step 2; 4, converting the tetrahedral mesh generated in the step 3 into an HEX8 hexahedral mesh; 5, converting the HEX8 hexahedral mesh generated in the step 4 into an HEX20 hexahedral mesh; 6, generating asimple geometric region grid; 7, generating a boundary layer grid near the surface of the fuel rod. The method solves the problems that computational fluid mechanics calculation software based on a spectral element method is difficult to establish a complex geometric model, and a complex geometric hexahedral mesh with a boundary layer cannot be generated.