SummaryTo improve the computational efficiency of the numerical manifold method for discontinuous deformation simulations, a spatial‐domain coupled explicit‐implicit time integration algorithm is proposed. A subdomain partition algorithm based on a super manifold element is developed for the numerical manifold method to simulate dynamic motions of blocky rock mass. In different subdomains, explicit or implicit time integration method is employed respectively based on its contact and motion status. These subdomains interact through assembling the corresponding explicit or implicit time integration‐based matrices of different rock blocks. The computational efficiency of the discontinuity system under dynamic loading is improved by partially diagonalizing the global matrices. Two verification examples of a sliding block along an inclined plane under a horizontal acceleration excitation and a multiblock system acted on by dynamic forces are studied to examine the accuracy of the proposed numerical method, respectively. A highly fractured rock mass situated on an inclined slope subjected to seismic excitations is then studied to show the computational efficiency of the developed algorithm. The simulated results are in good agreement with those from the versions using purely implicit or explicit time integration algorithm for the numerical manifold method. The computational efficiency is shown to be higher using the proposed algorithm, which demonstrates its potential for application in dynamic analysis of highly fractured rock masses.