Tensegrity structures are emerging as pivotal components in the assembly of ultralarge modular spacecraft in orbit, primarily due to their exceptional volume-to-mass ratio and robust controllability. During on-orbit operations, given the low damping and high flexibility of tensegrity, its vibration-induced deformations affect the magnitude of the heat flux, presenting a typical force–shape coupling problem. This paper introduces an energy-preserving matrix perturbation solution designed to efficiently and accurately address the thermally induced vibration challenges in tensegrity. This method effectively mitigates the energy dissipation and numerical instability issues. Furthermore, the analysis incorporates the impact of the axial component of heat flux on structural vibration, uncovering the influence mechanism of this often-overlooked slow variable on the dynamic behavior of tensegrity. The proposed method demonstrates a deviation of less than 1% between the thermal response and the results obtained from finite element analysis, while achieving a 70% reduction in computation time. The varying axial thermal load leads to a rapid decrease in system frequency, resulting in divergent thermal vibrations. Additionally, the significant dynamic stress can potentially surpass the structural stress limits. These findings underscore the critical importance of considering such effects in the design and calculation of tensegrity structures for aerospace applications.