To investigate the structural characteristics and phylogenetic relationships of the chloroplast genome of Cyclocarya paliurus (Batal.) Iljinskaja, this study used leaves of C. paliurus from Guangxin District, Shangrao City, Jiangxi Province as material. The complete chloroplast genome sequence was obtained through high-throughput sequencing, and its sequence characteristics, codon usage bias, and phylogenetic relationships were analyzed using bioinformatics methods. The results showed that the complete chloroplast genome of C. paliurus from Guangxin District, Shangrao City, was 160 992 bp in length, with an average GC content of 37.48%. A total of 133 genes were annotated, including 88 protein-coding genes, 37 tRNA genes and 8 rRNA genes. 84 simple sequence repeats (SSR) were identified, predominantly consisting of A/T repeats, along with 52 long repeats, mainly forward repeats and palindromic repeats. Comparison with 15 related species revealed that the gene types and arrangement order in the four boundary regions [LSC-IRB(JLB), SSC-IRB(JSB), SSC-IRA(JSA) and LSC-IRA(JLA)] of the C. paliurus chloroplast genome were largely consistent, with no significant differences in the extent of boundary expansion or contraction. Ten highly variable regions were identified in the LSC and SSC: matK_rps16, rps16_trnQ-UUG, psbK_psbI, trnS-GCU_trnG-GCC, trnT-GGU_psbD, ndhC_trnV-UAC, trnV-UAC, rpl22, ycf1, and rps15_ycf1. The overall codon usage bias in the C. paliurus chloroplast genome was weak and primarily influenced by natural selection. 15 optimal codons were identified: AAU, GAA, CAU, AAA, AUU, AUG, GGA, GGU, CCU, ACA, GUA, GUU, CGU, UUG and AGU, most of which end with U or A. Phylogenetic analysis indicated that C. paliurus from Guangxin District, Shangrao City, clusters closely with the diploid C. paliurus from Nanjing (MW531677, Cyclocarya paliurus isolate 2nPA), showing a close genetic relationship. The findings of this study provided a theoretical basis for research on genetic diversity, molecular breeding, and species identification of C. paliurus.