Background: Ankle sprains are very common in badminton, and chronic ankle instability (CAI) often develops in players after these injuries. CAI badminton players (CAIBP) are more susceptible to injuries during high-intensity tasks, such as jumping landings, due to decreased ankle stability. This study aims to explore the variations in lower limb biomechanics between CAIBP and normal badminton players (NBP) during single-leg medial landing tasks. Methods: Sixteen CAIBP and sixteen NBP university badminton players volunteered to participate in this experiment. The study used OpenSim open-source software to simulate and calculate lower limb joint angles, moments, and joint stiffness for the CAI group and healthy controls during a single-leg medial landing task, and utilized Delsys EMG to assess muscle pre-activation and activation levels. Independent samples t-tests and one-dimensional statistical parametric mapping were used to analyze the experimental results. Results: In terms of kinematics, before and after initial contact (IC) during landing, CAIBP showed significantly greater hip adduction and flexion angles than NBP (p < 0.001). Pre-IC, CAIBP exhibited less knee flexion (p = 0.004). Both pre- and post-IC, CAIBP exhibited significantly greater dorsiflexion angles (p = 0.045) and inversion angles (p < 0.001). In terms of muscle activation and dynamics, pre-IC, CAIBP had significantly less pre-activation of the peroneus longus than NBP (p = 0.007), and significantly more gastrocnemius lateral (p = 0.021) and gastrocnemius medial (p < 0.001) pre-activation. Post-IC, CAIBP had significantly greater muscle activation of the tibialis anterior (p < 0.001). Post-IC, peak knee extension moments (p = 0.012) and peak ankle plantarflexion moments (p = 0.001) were significantly greater in CAIBP than in NBP. In addition, CAIBP reported significantly higher knee stiffness (p = 0.001) and ankle stiffness (p < 0.001). Conclusions: During the medial landing task, CAIBP exhibited increased hip adduction and flexion, altered sagittal plane motion of the ankle, and increased activation of certain lower extremity muscles compared to NBP. Although these altered landing mechanisms contribute to enhanced stability during landing to some extent, they may also increase the potential risk of knee injury.