In this article, a series of nearly analytic symplectic partitioned Runge–Kutta (NSPRK) methods for the 3D seismic‐wave equation are developed. First, the Hamiltonian formulations for acoustic and elastic‐wave equations are presented, and then the spatial derivatives are discretized by a nearly analytic discrete operator to obtain a semidiscrete Hamiltonian system. The second‐, third‐, and fourth‐order symplectic partitioned Runge–Kutta schemes are then applied as the time integrator. A semianalytic procedure to facilitate the analysis of stability conditions and numerical dispersion relations is presented, and subsequent theoretical analysis shows that the NSPRK schemes preserve the wave velocity better than conventional symplectic schemes, especially on coarser grids. The numerical solutions computed by NSPRK schemes are compared with analytic solutions for the 3D acoustic and elastic cases. We implemented the NSPRK and some conventional schemes for a 3D acoustic wave propagation simulation in a parallel computer and compared their computational efficiencies. To generate comparable results, the NSPRK schemes require much less computer memory, central processing unit time, and communication time, which substantially accelerates the computation speed. The final simulation in the two‐layer acoustic model shows that the NSPRK schemes can suppress numerical dispersion and preserve the waveforms better than conventional symplectic schemes.