Circadian clocks are evolved to enhance the fitness of organisms by improving their ability to adapt to daily changes in environmental factors such as light, temperature and nutrients. How the robust circadian rhythm is maintained under different temperature and nutritional stress is still unclear. We found that the interaction between clock protein FRQ and its kinase CK1 is the key biochemical mechanism responsible for the temperature compensation in Neurospora crassa. Next, we also found that the nutrient sensing GCN2 signaling pathway is required for robust circadian clock function by regulating the histone acetylation at the clock gene frq locus under amino acid starvation in Neurospora crassa. Under amino acid starvation, the activation of GCN2 kinase and its downstream transcription factor CPC1 establish a proper chromatin state at the frq promoter by recruiting the histone acetyltransferase GCN5, which is important for circadian rhythm and metabolic homeostasis in response to amino acid starvation. In summary, we found the molecular mechanism of maintaining the robust circadian rhythm under temperature changes and amino acid starvation in Neurospora crassa.