Synonymous codons are not used with equal frequencies in most genomes. Codon usage has been proposed to play a role in regulating translation kinetics and co-translational protein folding. The relationship between codon usage and protein structures and the in vivo role of codon usage in eukaryotic protein folding is not clear. Here， we show that there is a strong codon usage bias in the filamentous fungus Neurospora. Importantly， we found genome-wide correlations between codon choices and predicted protein secondary structures: Nonoptimal codons are preferentially used in intrinsically disordered regions， and more optimal codons are used in structured domains. The functional importance of such correlations in vivo was confirmed by structure-based codon manipulation of codons in the Neurospora circadian clock gene frequency (frq). The codon optimization of the predicted disordered， but not well-structured regions of FRQ impairs clock function and altered FRQ structures. Furthermore， the correlations between codon usage and protein disorder tendency are conserved in other eukaryotes. Together， these results suggest that codon choices and protein structures co-evolve to ensure proper protein folding in eukaryotic organisms.