Abstract In this paper, we apply a simple finite element numerical scheme, proposed in an earlier work (Liu in Math Comput 70(234):579–593, 2000), to perform a high resolution numerical simulation of incompressible flow over an irregular domain and analyze its boundary layer separation. Compared with many classical finite element fluid solvers, this numerical method avoids a Stokes solver, and only two Poisson-like equations need to be solved at each time step/stage. In addition, its combination with the fully explicit fourth order Runge–Kutta (RK4) time discretization enables us to compute high Reynolds number flow in a very efficient way. As an application of this robust numerical solver, the dynamical mechanism of the boundary layer separation for a triangular cavity flow with Reynolds numbers Re = 104 and Re = 105, including the precise values of bifurcation location and critical time, are reported in this paper. In addition, we provide a super-convergence analysis for the simple finite element numerical scheme, using linear elements over a uniform triangulation with right triangles.