For many runners, mechanical characteristics of running shoes, such as cushioning ability, are important in finding their suitable shoes. In addition to that, subjective comfort has come to be regarded as a non-negligible factor these days. According to previous studies, it has been found that more comfortable shoe conditions are associated with less oxygen consumption and fewer injury frequencies as compared to the less comfortable shoe conditions. However, there is also the fact that the shoes that they feel comfortable with are different from runner to runner, and it still remains unclear why the runners consider their shoes comfortable. Therefore, in this study, we tried to find the differences between several groups with different shoe preferences, applying an equilibrium-point (EP)-based muscle synergy analysis to know the reason why runners consider the shoes comfortable. As a result of the study, it was found that ankle EP velocity could distinguish between the groups classified by shoe preference. This fact indicates that some force-related parameters calculated from posture and stiffness affect the feeling of comfort.