To illustrate the structure and sequence characteristics of chloroplast genome from Melicope pteleifolia, the leaf of M. pteleifolia was used for DNA isolation and library construction. The high-throughput sequencing was fulfilled by Novaseq platform, and then acquired sequence was assembled, annotated and analyzed using bioinformatics means. The results revealed that the chloroplast genome of M. pteleifolia was a circular quadripartite molecule with a size of 158 992 bp and encoded 134 genes. Altogether 86 simple sequence repeat was found in the plastome and the A/T mononucleotide was predominate type. Total 26 907 codon was screened out and those ended with A/T were frequently used. Sequence comparison demonstrated more divergence and occurred in non-coding region between M. pteleifolia and other Rutaceae species. Phylogenetic tree indicated various chloroplast genome sequences of M. pteleifolia shared close relationship and exhibited diversity in gene composition and base sequence.