Abstract: To analyze codon usage patterns and their underlying factors in the Hemsleya chinensis chloroplast genome, this study employed high-throughput sequencing to assemble and analyze the genome. The results revealed a typical quadripartite circular chloroplast genome structure with a total length of 157,735 bp and a GC content of 37.07%. Genome annotation identified 116 functional genes, of which 52 protein-coding sequences (CDS) were selected. A gradient decrease in the GC content across the three codon positions: GC₁ (46.53%), GC₂ (39.29%), and GC₃ (28.58%). The average effective number of codons (ENC) was 47.17, significantly higher than the conventional threshold of 35.00, while the codon adaptation index (CAI) ranged from 0.11 to 0.31. Natural selection was identified as the primary driver of codon usage bias. Through relative synonymous codon usage (RSCU) analysis, 14 optimal codons ending with A/U, such as GCA (Ala), UGU (Cys), and GAA (Glu), were identified.