Abnormal foot alignment such flatfoot is involved in running injuries. The mechanism by which flatfoot is susceptible to running injuries has not yet been established. The purpose of this study was to classify kinematic coupling patterns by hierarchical clustering, adding individuals with flatfoot and motion in the transverse plane involved in running injuries, and to identify the factors that determine the clusters classified. Twenty-four young healthy adults were divided and classified into normal and flat foot groups of 12 participants each, using the foot posture index. The task involved treadmill running. Cross-correlation coefficients between the ankle and knee joints and between the knee and hip joint were used to evaluate kinematic coupling in the sagittal, frontal, and transverse planes during the stance phase. Hierarchical clustering was used to classify kinematic coupling patterns using the cross-correlation coefficient as an input variable. After cluster classification, joint angles during the stance phase and static standing were compared between clusters. Hierarchical clustering classified kinematic coupling patterns between lower limb joints into two clusters, mainly the kinematic coupling on the frontal plane. However, clusters were not classified by foot alignment. Significant differences in knee varus/valgus, hip adduction/abduction, and internal/external rotation angles during the stance phase were observed between clusters. Foot alignment was not involved in the cluster analysis in this study. Further detailed evaluation of foot alignment is required.