This study investigates the thermal stress and bolt load distribution in a hybrid panel structure of an aircraft mechanical joint under extreme temperatures. The hybrid panel structure comprises two aluminum alloy splices, six T-shaped composite stringers, and two composite skins, secured together with 96 bolts. This study analyzed the strain induced by thermal stress on composite materials and metals within the structure across temperatures, employing temperature environment tests ranging from room temperature to −54 °C, alongside a carrying capacity test at −54 °C. Furthermore, a three-dimensional simulation model of the panel structure was developed, incorporating considerations for contact, metal elastoplasticity, and the progressive damage failure of composite materials. This model facilitated the determination of thermal stress and bolt load distribution patterns. The results indicate a strong consistency between the finite element analysis outcomes and the experimental data. Temperature variations exacerbate the uneven distribution of bolt loads, concentrating the load near the edges of the hybrid structure while diminishing it in the center. The bolt load distribution parallel to the mechanical load direction forms an “M” shape, with a maximum load magnitude of approximately 31 kN. Perpendicular to the mechanical load, the bolt load undergoes significant changes, especially at the edges, reaching a maximum of about 20 kN, which warrants attention. The bolt-load distribution of the structure with the increase in mechanical load at −54 °C tends to be consistent with that at room temperature.