Abstract: The codon usage bias in chloroplast genome of Michelia wilsonii was analyzed to reveal the main factors affecting it. First, the whole sequence of the M. wilsonii chloroplast genome was downloaded from the NCBI database for CDS sequence screening. Then CodonW 1.4.2 and EMBOSS were used to analyze the codon composition of the M. wilsonii chloroplast genome, to obtain GC content, ENC, RSCU, and other related parameters. Finally, neutral plot, ENC−plot, and PR2−plot analysis were performed to study the main factors of codon bias formation to obtain optimal codons. The results showed that the GC content of the third base of the codon in the chloroplast genome of M. wilsonii was low, with an average of 31.26%. ENC was between 36.36−57.89, indicating that the codon bias was weak, and ENC was significantly correlated with GC₂ and GC₃. There were 32 codons with RSCU > 1, 3 with G and C bases, and 29 with A and U bases. Its neutral plot, ENC−plot, and PR2−plot analysis showed that the codon usage bias of the chloroplast genome of M. wilsonii was mainly influenced mainly by selection pressure. Correspondence analysis showed that the gene sites encoding ribosomal proteins were dispersed, and the usage patterns of these gene codons were quite different, indicating that the expression rate of these genes in chloroplast genes of M. wilsonii was high. This study clarified that the main factor is selection pressure affecting the bias of the chloroplast codon usage in the M. wilsonii chloroplast genome. Finally, 14 optimal codons, including UUU, CUU, UCU, and so on, were selected from the chloroplast genome of M. wilsonii. They all end with bases A and U.