Abstract: Chouioia cunea belongs to the family Eulophidae and is an important endoparasitic natural enemy of the pupal stage of Hyphantria cunea. It possesses a high parasitism rate and strong fecundity. In this paper, the mitochondrial genome of Chouioia cunea was sequenced, assembled, and annotated using Illumina next-generation sequencing technology, and its structural characteristics and base composition were analyzed. The maximum likelihood method was employed to reconstruct the phylogenetic tree and analyze the phylogenetic relationships within Eulophidae. The results showed that the mitochondrial genome sequence of Chouioia cunea was 14,704 bp in length, including 13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes. The AT content of the whole genome sequence was 85.0%, indicating a significant AT bias. All 13 protein-coding genes have the typical ATN as the start codon and TAA as the stop codon. Except for the trnS1 and trnP genes, the secondary structures of the other 20 tRNAs exhibited a typical cloverleaf structure, and a U-U base mismatch was found in the secondary structure. Phylogenetic analysis indicated that all species of Eulophidae formed a single clade, supporting the monophyly of the family. Chouioia cunea is closely related to Tamarixia radiata in the phylogenetic tree. In this study, the mitochondrial genome structure and taxonomic status of Chouioia cunea were analyzed at the mitochondrial genome level, providing a theoretical basis for understanding the phylogenetic and evolutionary relationships of Eulophidae.