<p>Codon usage bias (CUB), referring to the unequal preference for synonymous codons in genetic coding, is shaped by both mutation pressure and natural selection. However, a comprehensive understanding of codon usage trends and the evolutionary mechanisms influencing the chloroplast, mitochondrial, and nuclear genomes of yellowhorn (<i>Xanthoceras sorbifolium</i> Bunge), a tree species native to China with high ecological and economic value, remains lacking. Analysis of nucleotide composition revealed a marked bias toward A/T bases, especially at the third codon position, across all three genomic types. Notably, nuclear genes had a relatively higher GC content compared to organellar counterparts. Analyses using ENC–GC3s plots, PR2-bias assessments, and neutrality plots consistently indicated that natural selection exerted a stronger influence than mutation in determining codon usage patterns. Additionally, correspondence analysis showed that only a limited portion of codon usage variation could be attributed to relative synonymous codon usage, implying the involvement of other evolutionary forces. We identified 11, 13, and 23 optimal codons in the chloroplast, mitochondrial, and nuclear genomes, respectively. Among these, CUU (Leu) and GCA (Ala) were consistently preferred across all compartments. Overall, our findings highlight genome-specific codon preferences and evolutionary pressures, underscoring distinct functional and evolutionary characteristics across the nuclear and organellar genomes.</p>