The sugarcane aphid, Melanaphis sacchari (Zehntner, 1897), is an agricultural pest that causes damage to plants in the Poaceae (the grasses) family, such as sorghum and sugarcane. However, genomic resources of this species are currently limited. Here, we used Nanopore long reads and Hi-C interaction map to generate a chromosome-level assembly with a total length of 356.1 Mb, of which 85.5% (304.6 Mb) is contained within the three autosomes and the X chromosome. Repetitive sequences accounted for 16.29% of the chromosomes and a total of 12,350 protein-coding genes were annotated, achieving 95.8% benchmarking universal single-copy orthologs (BUSCO) gene completeness. Phylogenomic analysis by comparing M. sacchari with twenty-four published aphid genomes representing three aphid tribes reveals that M. sacchari belongs to the tribe Aphidini and maintained a conserved chromosome structure with other Aphidini species. The genomic resources reported in this study will be useful for understanding the evolution of aphid genomes and studying pest management of M. sacchari.