SUMMARY Simulating poroelastic waves in large-scale 3-D problems having porous media coupled with elastic solids and fluids is computationally challenging for traditional methods. It is well established that the spectral element method (SEM) is more effective than the traditional methods like the finite element method (FEM) when dealing with complex geophysical problems, for its high-order accuracy with exponential convergence. However, at present, little research has been done for SEM in the frequency domain, which will be more efficient than the time-domain SEM for narrowband simulations with multiple sources, material dispersion and attenuation. Herein, we systematically develop a SEM in the frequency domain to simulate coupled poroelastic, elastic and acoustic waves in anisotropic (i.e. porosity, permeability and elastic coefficients with anisotropy), heterogeneous, and lossy media. Furthermore, we completely remove the dimension inconsistency between the displacement field and the pressure in porous media to reduce the condition number of the system matrix by around 16 orders of magnitude while maintaining the symmetry of the system matrix. To solve the multiphysics coupling problems, we apply different coupling conditions to different interface types, and use basis functions to discretize the corresponding governing equations. Numerical examples show that the proposed SEM can obtain higher accuracy with much fewer unknowns compared with the FEM and has the capacity to solve the large-scale real coupling problems.