In the calculation of Head-Related Transfer Functions (HRTFs) using the Boundary Element Method (BEM), the head surface of a subject needs to be discretized into boundary elements with specific impedance. To simplify HRTF calculation, a method for coupling Mesh Registration and BEM (MR-BEM) is proposed in this work, which means that a template mesh for calculation is established to register and generate the calculation mesh of a new head model, to replace the tedious operations of boundary conditions configuration. To validate the proposed method, the widely-used KEMAR artificial head model was adopted to compare the HRTFs of two groups of calculation meshes manually assigned and automatically registered impedance boundary conditions, respectively. Based on the inherent similarities in head shape and hair regions across individuals, the non-rigid impedance was set only for the hair region. Although the reflections from the non-rigid impedance of hair and clothes were shielded by pinnae in practice, this work just aims to validate the feasibility of the MR-BEM, which is significant for the simplification of BEM-based HRTF calculation.