Introduction: Foot progression angle affects gait and lowerlimb alignment. Altered angles may increase knee and ankle loading and produce tissue loading patterns previously linked to musculoskeletal injury. This study investigates how different foot progression angles modify knee and ankle biomechanics in young adults with flexible flatfoot. Methods: 28 participants (aged 18–35 years) with flexible flatfoot completed gait trials under three foot progression angle conditions. Kinematic and kinetic variables were analyzed using one-dimensional statistical parametric mapping. A 1D convolutional neural network was applied to classify progression angle patterns based on flexible flatfoot severity and gait biomechanics. Results: Decreasing foot progression angle reduced the ankle eversion/inversion range and knee abduction and external rotation (p < 0.05). Increasing foot progression angle lowered early stance ankle plantarflexion and increased knee abduction/external rotation (p < 0.05). Kinetically, a smaller foot progression angle reduced peak ankle plantarflexion moment and knee extension moment but increased the first peak of the knee adduction moment and rotational moment fluctuations (p < 0.05). A larger foot progression angle reduced rotational fluctuations and terminal stance knee extension moment (p < 0.05). The convolutional neural network model was most accurate for moderate flexible flatfoot cases, and ankle coronal and knee transverse biomechanics showed the strongest discriminative power. Conclusion: Modifying the foot progression angle can meaningfully alter knee and ankle loading in young adults with flexible flatfoot. Neutral or mild toe-in angles may help mitigate excessive eversion and rotational stress, suggesting a simple noninvasive adjustment that clinicians can incorporate during gait retraining or orthotic prescription. Because biomechanical responses vary across individuals, FPA modification may be the most effective when tailored to patient-specific gait characteristics. In addition, deep-learning-based gait classification shows promise for supporting personalized monitoring and guiding clinical decision-making during rehabilitation.