Guided modes of two-dimensional (2D) material-based plasmonic waveguides are applied in photonic devices because of their strong light-matter interaction within atomically thin layers and unique optical characteristics. Numerical simulations and experiments both play crucial roles in exploring unexpected phenomena at the sub-nanoscale of these materials. To efficiently and precisely compute mode characteristics, a multi-domain pseudospectral method (MPM) exhibiting high accuracy and fast convergence is proposed to study 2D material-based plasmonic waveguides in this study to alleviate the highly computational load of the widely used finite difference time domain or finite element method, as they demand extremely fine grid points or meshes around 2D materials. Models of graphene- and black phosphorus-based waveguides demonstrate that the MPM preserves exponential accuracy at relatively low computational cost, compared with the analytical characteristic equation and FEM, respectively. We believe that the proposed MPM offers a highly efficient and accurate approach to the study of 2D material-based photonics devices.