Skin necrosis is the most common complication in total auricular reconstruction, which is mainly induced by vascular compromise and local stress concentration of the overlying skin. Previous studies generally emphasized the increase in the skin flap blood supply, while few reports considered the mechanical factors. However, skin injury is inevitable due to uneasily altered loads generated by the intraoperative continuous negative suction and uneven cartilage framework structure. Herein, this study aims to attain the stable design protocol of the ear cartilage framework to decrease mechanical damage and the incidence of skin necrosis. Finite element analysis was initially utilized to simulate the reconstructive process while the shape optimization technique was then adopted to optimize the three-pretested shape of the hollows inside the scapha and fossa triangularis under negative suction pressure. Finally, the optimal results would be output automatically to meet clinical requirement. Guided by the results of FE-based shape optimization, the optimum framework with the smallest holes inside the scapha and fossa triangularis was derived. Subsequent finite element analysis results also demonstrated the displacement and stress of the post-optimized model were declined 64.9 and 40.1%, respectively. The following clinical study was performed to reveal that this new design reported lower rates of skin necrosis decrease to 5.08%, as well as the cartilage disclosure decreased sharply from 14.2 to 3.39% compared to the conventional method. Both the biomechanical analysis and the clinical study confirmed that the novel design framework could effectively reduce the rates of skin necrosis, which shows important clinical significance for protecting against skin necrosis.