Brown spot, a serious disease caused by Nothophoma quercina, results in small, brown, round-to-oval lesions on the leaves, and is a major concern in the pear industry. We previously reported a new pathogenic strain NqHH of Nothophoma quercina, which was isolated from ‘Huanghua’ pear (Pyrus pyrifolia Nakai, cv. Huanghua) leaves. However, genome information regarding this pathogen is limited. Herein, we detected the genome-wide sequence of NqHH strain using the Illumina NovaSeq 6000 and PacBio Sequel Ⅱ system. The genome of NqHH was estimated to be 35.3 Mb with an N50 length of 1.37 Mb, encoding for 11,659 predicted protein-coding genes. This genome sequence provides valuable information for the selection of pathogenic effectors and comparative genomics of brown spot disease in pears.