Background: Running is a widely practiced physical activity but carries a high risk of injury, with foot structure, particularly the medial arch, playing a vital role in biomechanical performance and injury prevention. As the core of foot support, the arch is essential for absorbing impact, transmitting force, and maintaining dynamic stability. This study aims to compare the dynamic stability of runners with moderate flatfoot and those with normal arches in the initial, steady, and fatigue stages in order to elucidate how fatigue differently affects their dynamic postural control. Methods: Twelve male runners were recruited. Using inertial measurement units (IMUs) and a Zebris treadmill system, data on Maximum Lyapunov Exponent(MLE) and plantar center of pressure (COP) trajectories were collected during the initial, steady-state, and fatigued phases. Results: In the fatigue phase, runners with flatfoot showed an increase of 0.05 s⁻¹ in short-term MLE compared to those with normal arches (p < 0.05), indicating significantly lower stability under fatigue. Conclusions: The deterioration of lower-limb dynamic stability in flatfoot runners is dependent on fatigue. Specifically, their overall lower dynamic stability stems primarily from a marked increase in MLE when entering the fatigued phase. Concurrently, fatigue induces alterations in COP trajectory and temporal gait parameters in flatfoot runners; they signify reduced efficiency in gait control.