To resolve stick insect phylogeny and mitochondrial rearrangement, mitochondrial genomes were sequenced. A total of ten mitochondrial genomes, 15,808–16,608 bp in length, were successfully sequenced in this study. Gene rearrangements were observed in three samples of two species: Paragongylopus plaumanni (sample number: WSZJC6 and YNZJC5), and Cnipsomorpha erinacea. The tandem duplication–random loss (TDRL) model provides a reasonable explanation for the detected gene rearrangements. Specifically, C. erinacea exhibits a gene rearrangement pattern of 12SrRNA-CR1-trnI-CR2-trnQ-trnM. P. plaumanni (WSZJC6) displays a CR-trnM-NCR-trnI-trnQ-ND2 gene arrangement, whereas P. plaumanni (YNZJC5) displays a more complex gene arrangement: a CR-trnM-NCR1-trnI-trnQ-NCR2-ND2. In addition to identifying novel gene structures, we analyzed codon usage and base composition across the 10 mitochondrial genomes. Bayesian inference (BI) and Maximum likelihood (ML) methods were employed to infer phylogenetic trees, utilizing the PCGs_123 and PCGs_12 datasets. When the unstable taxon Stheneboea repudiosa was excluded from the analysis, the subfamilies Lonchodinae and Necrosciinae were recovered as monophyletic. However, these two groups were not supported as sister lineages. Moreover, species Achrioptera manga was found to cluster with members of the family Bacillidae, resulting in the non-monophyly of both Phasmatidae and Bacillidae. The phylogenetic analysis of the three subfamilies within Pseudophasmatidae recovered the topology ((Pseudophasmatinae) + (Obriminae + Dataminae)), consistent with previous studies. Additionally, Heteropterygidae and Pseudophasmatidae formed a sister clade, while Necrosciinae and Phasmatidae formed another. Bacillidae was positioned between these two major clades, resulting in the overall topology: (Heteropterygidae + Pseudophasmatidae) + ((Bacillidae + (Necrosciinae + Phasmatidae)).