AbstractIn this paper, a high‐order compact finite difference method in general curvilinear coordinates is proposed for solving unsteady incompressible Navier‐Stokes equations. By constructing the fourth‐order spatial discretization schemes for all partial derivative terms of the pure streamfunction formulation in general curvilinear coordinates, especially for the fourth‐order mixed derivative terms, and applying a Crank‐Nicolson scheme for the second‐order temporal discretization, we extend the unsteady high‐order pure streamfunction algorithm to flow problems with more general non‐conformal grids. Furthermore, the stability of the newly proposed method for the linear model is validated by von‐Neumann linear stability analysis. Five numerical experiments are conducted to verify the accuracy and robustness of the proposed method. The results show that our method not only effectively solves problems with non‐conformal grids, but also allows grid generation and local refinement using commercial software. The solutions are in good agreement with the established numerical and experimental results.