Coptisplants (Ranunculaceae) contain high levels of isoquinoline alkaloids and have a long history of medicinal use.Coptisspecies are of great value in pharmaceutical industries and scientific research. Mitochondria are considered as one of the central units for receiving stress signals and arranging immediate responses. Comprehensive characterizations of plant mitogenomes are imperative for revealing the relationship between mitochondria, elucidating biological functions of mitochondria and understanding the environmental adaptation mechanisms of plants. Here, the mitochondrial genomes ofC. chinensis,C. deltoideaandC. omeiensiswere assembled through the Nanopore and Illumina sequencing platform for the first time. The genome organization, gene number, RNA editing sites, repeat sequences, gene migration from chloroplast to mitochondria were compared. The mitogenomes ofC. chinensis,C. deltoideaandC. omeiensishave six, two, two circular-mapping molecules with the total length of 1,425,403 bp, 1,520,338 bp and 1,152,812 bp, respectively. The complete mitogenomes harbors 68-86 predicted functional genes including 39-51 PCGs, 26-35 tRNAs and 2-5 rRNAs.C. deltoideamitogenome host the most abundant repeat sequences, whileC. chinensismitogenome has the largest number of transferred fragments from its chloroplasts. The large repeat sequences and foreign sequences in the mitochondrial genomes ofCoptisspecies were related to substantial rearrangements, changes in relative position of genes and multiple copy genes. Further comparative analysis illustrated that the PCGs under selected pressure in mitochondrial genomes of the threeCoptisspecies mainly belong to the mitochondrial complex I (NADH dehydrogenase). Heat stress adversely affected the mitochondrial complex I and V, antioxidant enzyme system, ROS accumulation and ATP production of the threeCoptisspecies. The activation of antioxidant enzymes, increase of T-AOC and maintenance of low ROS accumulation inC. chinensisunder heat stress were suggested as the factors for its thermal acclimation and normal growth at lower altitudes. This study provides comprehensive information on theCoptismitogenomes and is of great importance to elucidate the mitochondrial functions, understand the different thermal acclimation mechanisms ofCoptisplants, and breed heat-tolerant varieties.