Fluid–structure interaction (FSI) is a nonlinear multiphysics phenomenon that describes the interactions between incompressible fluid flows and immersed structures, making it invaluable to biomedical research. In this work, the common FSI methodologies in biomedical research were systematically summarized and classified into three groups based on FSI interfaces: fluid–channel interfaces, fluid–particle interfaces, and multi-interface interactions. A discussion of the role of the numerical FSI methods was also made, outlining its indispensable advantage in handling complex geometries, boundary conditions, and thus FSI interfaces. The applications of these methods are discussed in terms of blood vessel-related applications, drug-delivering micropumps, particle dynamics/cell sorting, and particle deformation and rapture. The development progress, current advances, and prospects of FSI's future application in biomedical research were illustrated. It was concluded that with the advances in computation technologies, the rapidly developing FSI methods can achieve state-of-the-art level details, helping to improve our understanding of various biomedical-related problems and the use of FSI techniques in biomedical research is likely to continue to grow.