This paper constitutes an extension of the work of Mendez, Gibaud & Nicoud: An unstructured solver for simulations of deformable particles in flows at arbitrary Reynolds numbers, Journal of Computational Physics, 256(1): 465-483 (2014), for three-dimensional simulations of deformable membranes under flow. An immersed thick boundary method is used, combining the immersed boundary method with a three-dimensional modeling of the structural part. The immersed boundary method is adapted to unstructured grids for the fluid resolution, using the reproducing kernel particle method. An unstructured finite-volume flow solver for the incompressible Navier-Stokes equations, is coupled with a finite-element solver for the structure. The validation process relying on a number of test cases proves the efficiency of the method, and its robustness is illustrated when computing the dynamics of a tri-leaflet aortic valve. The proposed immersed thick boundary method is able to tackle applications involving both thin and thick membranes/closed and open membranes, in significantly high Reynolds number flows and highly complex geometries.