The study dataset contains 21,964 viral contigs (Intertidal_viruses.fa), 20,102 vOTUs (Intertidal_vOTUs.fa), 238,445 vPCs (Intertidal_vPCs.gene and Intertidal_vPCs.protein), and 2,259 mOTUs (Intertidal_mOTUs.zip) obtained from 96 intertidal sediment metagenomes spanning 12 coastal regions from southmost to northmost in China. In addition, DOM tables (DOM_scaled_int_tab.csv) used in this study can also be obtained here. If this study dataset is useful, please cite: Ji et al. Biodiversity of mudflat intertidal viromes along the Chinese coasts. Nat Commun 15, 8611 (2024). https://doi.org/10.1038/s41467-024-52996-x For any other dataset/analysis inquiries, please contact me: jimengzhi@mail.sdu.edu.cn. The R code for this manuscript can be obtained from https://github.com/MengzhiJ.