Background: Fallopia aubertii (L. Henry) Holub is a perennial semi-shrub with both ornamental and medicinal value. The mitochondrial genomes of plants contain valuable genetic traits that can be utilized for the exploitation of genetic resources. The parsing of F. aubertii mitochondrial genome can provide insight into the role of mitochondria in plant growth and development, metabolism regulation, evolution, and response to environmental stress. Methods: In this study, we sequenced the mitochondrial genome of F. aubertii using the Illumina NovaSeq 6000 platform and Nanopore platform. We conducted a comprehensive analysis of the mitochondrial genome of F. aubertii, which involved examining various aspects such as gene composition, repetitive sequences, RNA editing sites, phylogeny, and organelle genome homology. To achieve this, we employed several bioinformatics methods including sequence alignment analysis, repetitive sequence analysis, phylogeny analysis, and more. Results: The mitochondrial genome of F. aubertii has 64 genes, including 34 protein-coding genes (PCGs), three rRNAs, and 27 tRNAs. There were 77 short tandem repeat sequences detected in the mitochondrial genome, five tandem repeat sequences identified by Tandem Repeats Finder (TRF), and 50 scattered repeat sequences observed, including 22 forward repeat sequences and 28 palindrome repeat sequences. A total of 367 RNA coding sites were predicted in PCGs, with the highest number (33) found within ccmB. Ka/Ks values estimated for mitochondrial genes of F. aubertii and three closely related species representing Caryophyllales were less than 1 for most of the genes. The maximum likelihood evolutionary tree showed that F. aubertii and Nepenthes \timesventrata are most closely related. Conclusions: In this study, we obtained basic information on the mitochondrial genome of F. aubertii and this study investigated repeat sequences and homologous segments, predicted RNA editing sites, and utilized the Ka/Ks ratio to estimate the selection pressure on mitochondrial genes of F. aubertii. We also discussed the systematic evolutionary position of F. aubertii based on mitochondrial genome sequences. Our study revealed variations in the sequence and structure of mitochondrial genomes in Caryophyllales. These findings are of great significance for identifying and improving valuable plant traits and serve as a reference for future molecular studies of F. aubertii.