The study of non-human multilevel societies can give us insights into how group-level relationships function and are maintained in a social system, but their mechanisms are still poorly understood. The aim of this study was to apply spatial association data obtained from drones to verify the presence of a multilevel structure in a feral horse society. We took aerial photos of individuals that appeared in pre-fixed areas and collected positional data. The threshold distance of the association was defined based on the distribution pattern of the inter-individual distance. The association rates of individuals showed bimodality, suggesting the presence of small social organizations or “units”. Inter-unit distances were significantly smaller than those in randomly replaced data, which showed that units associate to form a higher-level social organization or “herd”. Moreover, this herd had a structure where large mixed-sex units were more likely to occupy the center than small mixed-sex units and all-male-units, which were instead on the periphery. These three pieces of evidence regarding the existence of units, unit association, and stable positioning among units strongly indicated a multilevel structure in horse society. The present study contributes to understanding the functions and mechanisms of multilevel societies through comparisons with other social indices and models as well as cross-species comparisons in future studies.