This first randomized controlled trial in humans aimed to assess the efficacy and safety of low-dosage Escherichia coli-derived recombinant human bone morphogenetic protein 2 (ErhBMP-2)-incorporated biomimetic calcium phosphate coating-functionalized β-TCP (ErhBMP-2/BioCaP/β-TCP) as a novel bone substitute using the tooth-extraction-socket-healing model. Forty patients requiring dental implants after single-root tooth extraction were enrolled in this study and randomly assigned into three groups: ErhBMP-2/BioCaP/β-TCP (N = 15), β-TCP (N = 15) and natural healing (N = 10). New bone volume density from histomorphometric analyses was evaluated 6 weeks post-operatively as the primary outcome, and other histomorphometric analyses, alveolar bone and soft-tissue changes were the secondary outcomes. Safety parameters included adverse events, soft-tissue healing, oral health impact profile, serum BMP-2 concentrations and other laboratory tests. The findings revealed a significant increase in new bone volume density in patients treated with ErhBMP-2/BioCaP/β-TCP compared to those receiving β-TCP alone. The required bone augmentation procedures during implant placement surgery in the ErhBMP-2/BioCaP/β-TCP group were significantly less than in the natural healing group. There were no significant differences in safety parameters among the three groups. This clinical trial primarily proved the safety and efficacy of ErhBMP-2/BioCaP/β-TCP as a promising bone substitute.