Post and lintel frame is a prominent architectural structure in Chinese temple architecture, characterized by its wooden construction. Mortise–tenon joints (MTJs) serve as the primary connection method for these wooden structures, employing straight mortise nodes (SMNs) and through-mortise joints (TMNs). This study presents a method that utilizes wooden pins to reinforce MTJs, enhancing the seismic performance of timber frame structures. Finite element (FE) simulation verifies the effectiveness of wooden pins in reinforcing both SMNs and TMNs, leading to improved load-bearing capacity and ductility of the MTJs. Additionally, the study confirms that reinforced nodes help to restrict the displacement changes within the wooden frame. The paper also investigates the optimal distribution of MTJs reinforced by the wooden pins throughout the structure, with the aim of enhancing the wood frame’s seismic performance. The results show the bearing capacity of MJT reinforced with wooden pins is approximately 11.3% higher compared to that of MTJ without reinforcement. The reinforcement of wood pins effectively controls the horizontal displacement of the overall structure of the wooden frame, which is reduced by about 50%–62% compared with the unreinforced wooden frame. The locating the wooden pin-reinforced MTJs in the outer columns and middle layer columns reduces the structural displacement, which is 31.53% in X direction, 5% in Y direction, and 25.86% in Z direction.