As an emerging cycle technology, the supercritical carbon dioxide (sCO2) Brayton cycle system has gained significant attention due to its compact structure and high efficiency. It offers a promising solution to address the extreme thermal environments encountered by hypersonic aircraft during operation. The compressor, one of core components of the cycle system, is susceptible to causing pressure and temperature fluctuations in the internal working medium (sCO2) during high-speed operation, which will induce non-equilibrium condensation. This phenomenon increases compressor operation’s instability, adversely affecting the cycle system’s efficiency and reliability. Firstly, this work reviews the research progress of sCO2 Brayton cycle systems in waste heat utilization for hypersonic aircraft. Subsequently, it examines the current research status on non-equilibrium condensation within compressors and highlights the challenges faced in sCO2 phase transition theory. Finally, the work looks forward to the potential applications of sCO2 Brayton cycle systems in hypersonic aircraft thermal protection and emphasizes the necessity of suppressing non-equilibrium condensation in compressors to enhance system reliability. The findings of this study provide references for the design and optimization of thermal protection technologies and sCO2 Brayton cycle compressors for hypersonic aircraft.