Our ultimate goal is to analyze the flapping-wing motion of a free-flying insect as a fluid–structure interaction (FSI) phenomenon. Numerical methods for handling moving boundaries in FSI analysis can be broadly classified into tracking and capturing methods. The tracking method, however, often leads to distorted meshes in the fluid domain, causing instability due to the large deformations, movements, and contact of boundaries inherent in flapping motion. In contrast, the capturing method is robust against such complex boundary motions but struggles to maintain high-resolution boundary layer meshes, resulting in reduced accuracy. To address these challenges, we employ structured meshes based on the interface capturing method. For achieving flexible local high-resolution in specific regions, we explore the application of the s-version of the finite element method (SFEM) [1]. SFEM enables efficient modeling by superimposing meshes with different spatial resolutions, offering advantages such as localized high accuracy, reduced computational cost, and simplified meshing procedures. As an initial step, we have developed a B-spline-based SFEM (BSFEM) [2], which integrates both B-spline and Lagrange basis functions, significantly enhancing accuracy and convergence. This study finally aims to refine local mesh adaptation in interface capturing approaches for moving boundary problems in fluid dynamics. As a next step, BSFEM is applied to fluid problems for localized refinement, and Nitsche’s method is incorporated to enforce boundary conditions at the boundary in the local region. Nitsche’s method provides significant numerical advantages: it ensures variational consistency and stability, maintains the symmetry of the system, and preserves the original degrees of freedom without requiring additional variables such as Lagrange multipliers. The proposed approach is validated through several 3D flow test cases. [1] Jacob Fish. The s-version of the finite element method, Computers & Structures, 43(3):539–547, 1992. [2] Nozomi Magome, Naoki Morita, Shigeki Kaneko, and Naoto Mitsume. Higher-continuity s-version of finite element method with B-spline functions, Journal of Computational Physics, 497:112593, 2024.