Uncontrollable bleeding and tissue defects caused by trauma are significant clinical issues. Apoptotic vesicles (apoVs) derived from mesenchymal stem cells (MSCs) have shown promise for hemostasis and tissue regeneration, but their clinical safety and efficacy remain unverified. We investigated the procoagulant and regenerative function of lyophilized MSC-derived apoVs (MSC-apoVs) using in vitro experiments and in vivo rat models. In addition, we conducted a double-blind, randomized, self-controlled clinical trial to evaluate the safety and efficiency of lyophilized MSC-apoVs for hemostasis and bone regeneration following extraction of impacted mandibular third molars. We show that lyophilized MSC-apoVs maintain their procoagulant and regenerative functions after storage at 4°C for 3 months and upregulate tripartite motif containing 71 (TRIM71) to activate the extracellular signal-regulated kinase (ERK) signaling pathway. Furthermore, among the 43 enrolled subjects, 39 patients completed all follow-ups and 4 patients were lost to contact. All 39 patients tolerated MSC-apoVs well, with no serious adverse events or abnormal blood test results observed. The MSC-apoV group exhibited shortened hemostatic time and accelerated alveolar bone regeneration compared to the control group. This is the first clinical study to demonstrate that apoVs are safe, well-tolerated, and effective as a cell-free biological therapy for hemostasis and bone regeneration.