This study aimed to establish a risk prediction nomogram model for anterolateral, mediolateral, and posterolateral ankle pain in patients with chronic ankle instability (CAI) and analyse the risk factors for pain at different ankle sites. Thirty runners with CAI who reported ankle pain in the anterolateral, mediolateral, or posterolateral regions were recruited for this study. Kinematic, kinetic, and electromyographic data during running were collected using motion capture system, etc. These data were used to generate a dynamic nomogram. The results showed that anterolateral ankle pain in patients with CAI may be caused by insufficient gastrocnemius muscle strength (OR = 0.85, 95% CI: 0.73 ~ 0.97), excessive ground reaction force (GRF, OR = 2.64, 95% CI: 1.25 ~ 6.22), and an increased percentage of ankle energy absorption (OR = 9.11, 95% CI: 1.50 ~ 77.79). Mediolateral ankle pain might be contributed by greater ankle inversion angle (OR = 1.08, 95% CI: 1.01 ~ 1.00) and GRF (OR = 2.13, 95%CI: 1.17 ~ 4.31). Moreover, posterolateral ankle pain was predicted by increased ankle internal rotation angle (OR = 1.06, 95% CI: 1.00-1.12), increased GRF (OR = 2.16, 95% CI: 1.07–4.80), and decreased dynamic stability (OR = 0.20, 95% CI: 0.05–0.68). To prevent ankle pain, patients with CAI should be encouraged to focus on improving the neuroreceptor sensitivity of the gastrocnemius muscles, and retraining their energy absorption patterns.