(1) The Hoop Head Tenon-mortise Joint (HHTMJ) in the Tusi Manor in Tibetan areas in Yunnan, China, has a serious decay phenomenon. To understand the effect of decay on the seismic performance of HHTMJ, (2) the five groups of HHTMJ and small-size Pinus kesiya var. langbianensis wood mechanical property testing specimens were placed in an artificially set decay environment and cultivated together with wood decay fungi for 0, 6, 12, 18, and 24 weeks, respectively. Low-cycle repeated loading tests were conducted to compare the failure mode, hysteresis curve, skeleton curve, and cumulative energy consumption of the HHTMJ under different decay cycles. (3) The results indicate that the failure mode of the HHTMJ is fractured at the tenon shoulder, and the deformation and failure of the tenon increase with the increase in decay. Compared with the non-decayed specimens, the ultimate bearing performance of the specimens after 6, 12, 18, and 24 weeks of decay decreased by 8.83%, 16.97%, 19.69%, and 30.22%, respectively. The cumulative energy consumption decreased by 21.6%, 27.4%, 33.2%, and 41.3%, respectively. (4) Decay primarily occurs on the exterior of the tenon, with minimal decay on the interior. The degradation of seismic performance in HHTMJ is relatively close to the degradation observed in small-size wood specimens during mechanical property testing.