Extracellular vesicles (EVs) contain proteins, enzymes and metabolites that contribute to the therapeutic potential of human mesenchymal stem cells (hMSCs). However, scale-up production of hMSC EVs has become a major challenge. In current study, hMSCs were grown as 3D aggregates under wave motion to promote EV secretion (3D EVs). mRNA sequencing reveals global transcriptome alterations (e.g., upregulated Wnt, TNF, and Hippo signaling and downregulated cellular senescence) for 3D aggregates. Compared to 2D EVs, the quantity of 3D EVs was enhanced significantly with smaller size, higher miR-21 and miR-22 expression, and the altered protein cargo revealed by proteomics. 3D hMSC aggregates promote activation of the endosomal sorting complexes required for transport (ESCRT) pathway and ESCRT-independent pathway. In addition, 3D EVs rejuvenated stem cells expressing cellular senescence and modulated immune response determined by T lymphocyte and macrophage phenotype assays. In summary, this study provides a promising strategy for high-quality EV production from hMSCs with enhanced therapeutic potentials.