Abstract The therapeutic potential of extracellular vesicles (EVs) in bone regeneration is noteworthy; however, their clinical application is impeded by low yield and limited efficacy. This study investigated the effect of low‐intensity pulsed ultrasound (LIPUS) on the therapeutic efficacy of EVs derived from periodontal ligament stem cells (PDLSCs) and preliminarily explored its mechanism. PDLSCs were cultured with osteogenic media and stimulated with or without LIPUS, and then EVs and LIPUS‐stimulated EVs (L‐EVs) were isolated separately. We investigated the biological characteristics and effects of these two EVs on cell proliferation, migration, osteogenic differentiation, and bone regeneration in vivo and in vitro, and explored the potential mechanism by analyzing protein profiles. LIPUS significantly stimulated the secretion of PDLSCs‐EVs, and L‐EVs exhibited stronger efficacy in promoting cell proliferation, migration, and osteogenic differentiation, thereby enhancing new bone formation. LIPUS stimulation affected the protein profile of PDLSCs‐EVs, and 42 proteins were upregulated and 4 proteins downregulated in L‐EVs when compared with EVs. LIPUS significantly upregulated the level of cartilage oligomeric matrix protein (COMP) in EVs, which enhanced EVs' osteogenic ability via the PI3K/AKT pathway. This study proposes that LIPUS has potential as an optimization method for enhancing the therapeutic effects of EVs in tissue regeneration.