Currently, the study of analytical solutions for the seismic stability of slopes under anchorage conditions is one of the hottest subjects in engineering. In this paper, an analytical solution for the seismic safety of the three-dimensional (3D) two-stage rock slope reinforced with prestressed anchor cables governed by the nonlinear Hoek–Brown criterion was deduced, in which the analyses of seismicity were performed by the latest modified pseudo-dynamic method. This method supplements the consideration of the damping effect of the rock medium on seismic waves, which is more in line with the real seismic situation. A mathematical geometric model was developed for calculating the external forces work and internal energy dissipation acting on 3D rotating rock masses reinforced with prestressed anchor cables, in which the seismic work rate was calculated using a new layer-by-layer superposition summation method. The analytical solution of the safety factor could be collated as an explicit function of several variables, and then, the optimal value was obtained by the Particle Swarm Optimization (PSO) algorithm. To corroborate the accuracy of new analytical solutions, the results were contrasted with those of the pertinent literature. The results of the two comparisons were very close. Ultimately, the sensitivity analyses and coupling effects of seismic pseudo-dynamic factors and prestressing anchorage factors were carried out. It was found that even small seismic intensities had a large effect on the stability of rock slopes with developed joints. Increasing the number of steps and prestressing anchors can effectively improve the stability of rock slopes under seismic effects. The conclusions have significant implications for the anchorage design of the 3D two-stage rock slope as seismic events occur.