The hoverfly, Eupeodes corollae (Diptera: Syrphidae), is an economically important insect that provides dual ecosystem services including aphid control and pollination. Here we present a 595-Mb chromosome-level reference genome of E. corollae with contig N50 length of 1,794 kb. With Hi-C scaffolding, about 570.8 Mb (96.0%) of the assembled contigs were anchored into 4 chromosomes, and 51.47% repeat sequences and 23,374 gene models were predicted in the genome. Comparative genomics reveals significant expansion of digestive enzyme gene families in E. corollae compared to other dipteran species. Furthermore, there was also significant expansion of cytochrome CYP6 subfamily genes in E. corollae, with tandem arrangements on the genome. Several digestive enzymes with high expression levels at the larval stage might be related to aphid digestion. The high quality of the E. corollae genome assembly will help us understand its pest control mechanisms and pollination behaviors and provide a reference for other natural enemies of pests and promoting the use of beneficial insects.