A spatial modes filtering finite-element time-domain method with nonuniform subgridding mesh (NUSSMF-FETD) is proposed to enhance the modeling flexibility and computation efficiency of electromagnetic simulations with fine structures. Taking the nonuniform rectangular meshes as local refinement elements causes complex edge distributions in subgridding elements, the element and system matrices construction process of nonuniform subgridding FETD (NUS-FETD) is given in detail. Then the NUSSMF-FETD is obtained by introducing the spatial modes filtering (SMF) method. NUS-FETD effectively reduces the unknowns in local refinement regions compared to the uniform subgridding FETD (US-FETD). On this basis, NUSSMF-FETD can expand the time step and also keep computation accurate and efficient. The NUSSMF-FETD based on local eigenvalue solution (LES-NUSSMF-FETD) further reduces the time and memory consumption of system eigenvalue analysis. Numerical results present that the NUSSMF-FETD method has high spatial modeling flexibility and computation efficiency.