Objective To study the influence of different trajectories of 3-PH/R ankle rehabilitation robot on joints and muscles. Methods The 3-PH/R ankle rehabilitation robot was simplified and imported into biomechanical modeling software by analyzing the kinematics principles. Using the actual motion trajectory of ankle rehabilitation robot as model driving, the joint and muscle forces were compared under three different trajectories, namely, dorsiflexion/plantarflexion, inversion/eversion and nutation. The correlation analysis on three motion trajectories was conducted. Results Nutation could satisfy the function of both plantar dorsiflexion/plantarflexion, and inversion/eversion, and made the ankle muscles fully exercised. The maximum difference in joint force under three different rehabilitation trajectories was 0.3 N. Different muscles had different sensitivity to trajectories. Conclusions The continuous dynamic analysis of muscle force and joint force under three kinds of rehabilitation trajectories was implemented. The results have certain theoretical significance and clinical reference value for the clinical application of ankle rehabilitation robot and the formulation of rehabilitation trajectory.