Alpinia oxyphylla Miq. renowned as one of the "Four Great Southern Medicinal Herbs" of China, possesses modern pharmacological activities including antioxidant, anti-inflammatory, neuroprotective, and anti-tumor effects. However, with its wild resources increasingly depleted and cultivated plants facing pressures from pests, diseases, and climate change, there is an urgent need to enhance germplasm quality and stress resistance through biotechnological approaches. This study aimed to analyze the codon usage bias in the chloroplast genome of A. oxyphylla Miq. providing a theoretical basis for its subsequent applications in genetic engineering and synthetic biology. Fifty-one high-quality protein-coding sequences from the A. oxyphylla chloroplast genome were screened based on multiple filtering criteria. Codon usage characteristics were analyzed using CodonW 1.4.2 software combined with the online platform CUSP. There existed significant A/U-ending preference. The GC content showed a decreasing gradient (GC₁=45.69%>GC₂=38.79%>GC₃=27.50%), with 90.6% of the preferred codons (RSCU>1) ending in A/U. There existed overall weak codon usage bias. The mean effective number of codons (ENC) was 46.56 (67.78% of genes had ENC>45), and the mean codon adaptation index (CAI) was 0.17. Natural selection dominated codon evolution. Neutrality plot analysis showed no significant correlation between GC₁₂ and GC₃. The actual values significantly deviated from the expected curve in the ENC-plot. The PR2-plot revealed a bias at the GC₃ position favoring A>T and C>G. Ten optimal codons were identified. This study is the first to reveal the conserved A/U-ending preference and the multifactor synergistic regulatory mechanism dominated by natural selection in the A. oxyphylla chloroplast genome. The identified optimal codons could serve as key elements for chloroplast genetic engineering in A. oxyphylla. Directional optimization of codon usage in exogenous genes (e.g., genes encoding enzymes for medicinal compound synthesis) using the codons is expected to enhance the expression efficiency, providing technical support for A. oxyphylla quality improvement and stress-resistant breeding.