Circadian clocks enable plants to predict temperature changes and adapt to the living climate, known as temperature entrainment and temperature compensation (TC), with largely unrevealed mechanisms. Here, we proposed that the circadian component PRR9 (PSEUDO-RESPONSE REGULATOR 9) has evolved for thermal adaptation by acting as a hub factor in transmitting temperature input and maintaining TC. High temperature promotes PRR9 protein accumulation and triggers liquid-liquid phase separation, which not only directly inhibits the transcription level of CCA1 but also facilitates the recruitment of ALKBH9B to remove m⁶A installation and accelerates CCA1 mRNA degradation. Moreover, we proposed a phyB-PRR9 thermoregulatory module to transmit progressively rising temperature via temperature-dependent interacting compartment alteration that regulates the repressive phase and activity of PRR9. Our findings unmasked plants that possess intricate high-temperature sensing mechanisms for adaptation to warming climates, laying a foundation for engineering thermo-resilient crops.