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Modern sugarcane cultivars are highly polyploid with complex nuclear genomic genetic background, while their mitochondrion (mt) genomes are much simpler, smaller and more manageable and could provide useful phylogenetic information. In this study, the mt genome of a modern commercial cultivar A1 was sequenced via Illumina Hiseq XTen and PacBio Sequel platform. The assembled and annotated mitochondrial genomes of A1 were composed of two circular DNA molecules, one large and one small, which were named Chromosome 1 and Chromosome 2. The two distinct circular chromosomes of mitogenome construct is consisted with other sugarcane cultivars i.e., <i>Saccharum officinarum</i> Khon Kaen 3 and <i>Saccharum</i> spp. hybrids ROC22 and FN15. The Chromosome 1 of A1 mitogenome is 300,822 bp in length with the GC content of 43.94%, and 7.14% of Chromosome 1 sequences (21,468 nucleotides) are protein coding genes (PCGs) while 92.86% (279,354 nucleotides) are intergenic region. The length of Chromosome 2 is 144,744 bp with the GC content of 43.57%, and 8.20% of Chromosome 2 sequences (11,865 nucleotides) are PCGs while 91.80% (132,879 nucleotides) are intergenic region. A total of 43 genes are located on Chromosome 1, which contains 22 PCGs (six <i>nad</i> genes, four <i>rps</i> genes, four <i>atp</i> genes, three <i>ccm</i> genes, three <i>cox</i> genes, one <i>mat</i> gene and one <i>mtt</i> gene) and 21 non-coding genes including 15 tRNAs and 6 rRNAs. Chromosome 2 includes 18 genes in total, which contains 13 PCGs (four <i>nad</i> genes, three <i>rps</i> genes, two <i>atp</i> genes, one <i>ccm</i> gene, one <i>cob</i> gene, one <i>cox</i> gene and one <i>rpl</i> gene) and five non-coding genes (tRNA genes). Analysis of codon usage of 35 PCGs showed that codon ending in A/U was preferred. Investigation of gene composition indicated that the types and copy numbers of CDS genes, tRNAs and rRNAs of A1 and FN15 were identical. The <i>cox1</i> gene has two copies and the <i>trnP</i> gene has one copy in A1, FN15 and ROC22 three lines, while there is only one copy of <i>cox1</i> and two copies of <i>trnP</i> in <i>S. officinarum</i> Khon Kaen 3. In addition, <i>S. officinarum</i> Khon Kaen 3 have no <i>nad1</i> gene and <i>rps7</i> gene. 100 sequence repeats, 38 SSRs and 444 RNA editing sites in A1 mt genome were detected. Moreover, the maximum likelihood phylogenetic analysis found that A1 were more closely related to <i>S.</i> spp. hybrid (ROC22 and FN15) and <i>S. officinarum</i> (Khon Kaen 3). Herein, the complete mt genome of A1 will provide essential DNA molecular information for further phylogenetic and evolutionary analysis for <i>Saccharum</i> and Poaceae.