Human respiratory microbiome plays a crucial role in respiratory health, but there lack a comprehensive respiratory genome catalogue to study the microbiome. In this study, we collected whole-metagenome shotgun sequencing data of 4,067 samples, and sequenced long reads of 124 samples, leading 9.08 Tbp short-read and 0.42 Tbp long-read data, respectively. The data, integrated with a novel assembly algorithm, enables us to obtain a comprehensive human respiratory genome catalogue (RGC). This RGC displays high quality, with 190,443 contigs over one Kbps and an N50 length exceeding 13 Kbps; it comprises 159 high-quality and 393 medium-quality genomes, including 117 previously uncharacterized respiratory bacteria. To facilitate respiratory microbiome study, we present three important archives for RGC applications, including genome sequences, gene sequences in GBK format, taxonomical profile, ARG profile, VG profile, and MGC profile.