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The southern giant petrel <i>Macronectes giganteus</i>, a large seabird of the southern oceans, is one of only two members of the genus <i>Macronectes</i> and is the largest species in the order Procellariiformes. Although these two families account for the vast majority of the avian fauna inhabiting the Antarctic and sub-Antarctic regions, studies on the status of some populations and the associated genetic data are currently extremely limited. In this study, we assembled the genome of <i>M. giganteus</i> by integrating Pacific Biosciences single-molecule real-time sequencing and the Chromium system developed by 10x Genomics. The final <i>M. giganteus</i> genome assembly was 1.248 Gb in size with a scaffold N50 length of 27.4 Mb and a longest scaffold length of 120.4 Mb. The <i>M. giganteus</i> genome contains 14,993 predicted protein-coding genes and has 11.06% repeat sequences. Estimated historical effective population size analysis indicated that the southern giant petrel underwent a severe reduction in effective population size during a period coinciding with the early Pleistocene. The availability of this newly sequenced genome will facilitate more effective genetic monitoring of threatened species. Furthermore, the genome will provide a valuable resource for gene functional studies and further comparative genomic studies on the life history and ecological traits of specific avian species.