This study investigated how prolonged outdoor marathon running alters stance-phase rearfoot symmetry and explored the mechanism of symmetry changes using dual wearable wireless inertial measurement units (IMUs). Kinematic data from 23 male runners (45 ± 6 years) were collected continuously during an outdoor marathon using bilateral rearfoot-mounted nine-axis IMUs. The normalized symmetry index of stance-phase kinematics was analyzed via statistical parametric mapping to compare pre- and post-race asymmetry. Participants demonstrated significant prolonged running-induced increases in rearfoot asymmetry across multiple gait metrics:​ sagittal-plane rotation at initial contact (0–3 % stance phase, p = 0.005), vertical acceleration at mid-stance (34–36 % stance phase, p = 0.005), medial–lateral acceleration (55–66 % and 81–89 % stance phase, p = 0.005), and transverse-plane rotation (62–98 % stance phase, p = 0.005) during propulsion. The decreased symmetry was predominantly driven by three dominant-rearfoot adaptations:​ heightened lateral acceleration (e.g. 0.14 g vs. 0.37 g at 60 % stance;​ p = 0.005), reduced superior acceleration (e.g. 0.89 g vs. 0.52 g at 36 % stance;​ p = 0.005), and elevated external rotation velocity (16.95°/s vs. 49.75°/s at 70 % stance;​ p = 0.005). The findings suggested a compensatory shift toward dominant-limb reliance during prolonged running, characterized by asymmetric propulsion mechanics. While this adaptation may help sustain performance, it redistributes biomechanical workload unevenly, disproportionately loading the dominant limb during critical phases like propulsion. Monitoring rearfoot asymmetry using wearable IMUs provides a practical method for early detection of fatigue-related compensatory patterns, enabling timely interventions to prevent injury and optimize performance in marathon runners.