Objective This study investigated lower limb biomechanics and lateral asymmetry during the continuous vertical jump (CVJ) landing process in individuals with unilateral functional ankle instability (FAI) and compared these characteristics with those of healthy individuals. Methods Fourteen males with unilateral FAI were selected as the experimental group, and 14 males without ankle joint injury were matched to the control group. Both the groups performed 30 CVJ landing tasks. Lower limb kinematic and kinetic characteristics during the 1st, 15th, and 30th CVJ landings were synchronously collected using Vicon and Kistler equipment, and a 2 × 3 mixed analysis of variance was adopted for the data. Results In the execution of CVJ landing tasks, patients with FAI demonstrated no significant differences in the kinematic and kinetic characteristics of the affected limbs compared with healthy controls. However, a greater degree of lateral asymmetry was observed in the FAI group, particularly in the symmetry index (SI) of the vGRF peak. Despite the increase in the number of jump landings and consequent increase in fatigue levels, which led to adjustments in lower limb movement patterns, these adjustments did not appear to have a significant impact on the biomechanical characteristics and asymmetry of the affected limb in patients with FAI. Conclusions This study provides a theoretical basis for the prevention of recurrent ankle sprains in patients with FAI, as well as rehabilitation training prior to their return to sports. These findings underscore the importance of addressing lower limb asymmetry in the rehabilitation training of patients with FAI to reduce the risk of potential long-term injuries. When formulating rehabilitation plans for patients with FAI, particular attention should be paid to the correction of lower limb asymmetry with consideration of biomechanical adaptability under different states to achieve a more comprehensive rehabilitation outcome.