<p>Lip incompetence is an esthetic orthodontic problem, but its functional relevance during mastication remains unclear. This study aimed to develop an objective system for assessing three-dimensional facial dynamics during mastication and to compare facial soft-tissue coordination and lip-closure force between individuals with and without lip incompetence. Thirty-nine children aged 6–12 years were classified into a lip-incompetence group (<i>n</i> = 16) and a control group (<i>n</i> = 23). Participants chewed gum unilaterally while 3D facial images were recorded. A homologous wire-mesh model was generated for each frame, and elastic energy based on inter-point displacement was calculated for the upper and lower lips. After regional averaging and normalization, the time-integrated difference between normalized mean elastic energies of the upper and lower lips was defined as the Surface Synchrony Index (SSI), representing lip-movement coordination rather than strict temporal phase synchronization. Lip-closure force was also measured. SSI was significantly higher in the lip-incompetence group than in the control group, indicating reduced coordination between upper and lower lip movements during mastication. In contrast, no significant difference in lip-closure force was observed between groups. These findings indicate that lip incompetence was associated with impaired coordination of facial soft-tissue movements during mastication. Static observation and lip-closure force alone are insufficient to evaluate functional problems during mastication. Surface-based kinematic indices enable objective assessment of difference in facial soft-tissue coordination associated with lip incompetence and may provide clinically relevant information for functional evaluation.</p>