Massive studies have explored biological motion (BM) crowds processing for their remarkable social significance, primarily focused on uniformly distributed ones. However, real-world BM crowds often exhibit hierarchical structures rather than uniform arrangements. How such structured BM crowds are processed remains a subject of inquiry. This study investigates the representation of structured BM crowds in working memory (WM), recognizing the pivotal role WM plays in our social interactions involving BM. We propose the group-based ensemble hypothesis and test it through a member identification task. Participants were required to discern whether a presented BM belonged to a prior memory display of eight BM, each with distinct walking directions. Drawing on prominent Gestalt principles as organizational cues, we constructed structured groups within BM crowds by applying proximity and similarity cues in Experiments 1 and 2, respectively. In Experiment 3, we deliberately weakened the visibility of stimuli structures by increasing the similarity between subsets, probing the robustness of results. Consistently, our findings indicate that BM aligned with the mean direction of the subsets was more likely to be recognized as part of the memory stimuli. This suggests that WM inherently organizes structured BM crowds into separate ensembles based on organizational cues. In essence, our results illuminate the simultaneous operation of grouping and ensemble encoding mechanisms for BM crowds within WM.