In this study, we investigated the development of advanced testing methodologies for evaluating the mechanical properties of ceramic crown crack-repair systems, alongside the characterization of hydroxyapatite (HA) thin films deposited by vacuum coating technology for antibacterial and biocompatibility applications. These innovations are aimed at addressing common clinical challenges, including variability in technician-fabricated prostheses, crown surface cracking caused by mastication, and insufficient antibacterial performance. A nanomedical resin reinforced with inorganic nanopowders was developed, and the Taguchi quality engineering method using an L9(33) orthogonal array was employed to determine the optimal processing parameters. The optimal formulation consisted of 2 wt% SiO2 nanopowder and a baking temperature of 100 ℃, resulting in the highest compressive strength. In addition, HA thin films deposited by RF magnetron sputtering exhibited excellent adhesion performance corresponding to HF2–HF3 levels satisfying the VDI 3198 standard. Antibacterial evaluation demonstrated that the HA-coated crown specimens achieved 64.33–85.23% greater antibacterial effectiveness than uncoated specimens. Furthermore, biocompatibility testing using MG-63 cells revealed cell viability exceeding 90% after five days for coatings deposited at 100 or 150 W for 60 min, confirming their non-cytotoxic characteristics. These findings demonstrate that the combination of optimized nanomedical resin repair and HA surface functionalization significantly enhances the mechanical strength, antibacterial performance, and biocompatibility of ceramic crown restoration systems.