Highlights • This study systematically analyzed alterations in the ocular surface microbiome of patients with progressive supranuclear palsy-Richardson’s syndrome (PSP-RS) via metagenomic sequencing, with comparisons to Parkinson’s disease (PD) patients and healthy controls (HC). • The β-diversity of the ocular surface microbiome in PSP-RS patients was significantly altered compared to HC, while no such obvious difference was observed in PD patients. PSP-RS patients exhibited increased abundances of g_Acinetobacter and g_Anaerococcus, decreased abundance of g_Vibrio, as well as characteristic changes at the specific species (e.g., s_Acinetobacter_guillouiae) and strain levels. • The ocular surface microbiome of PSP-RS patients showed more significant remodeling in Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional pathways, involving multiple key pathways such as transposase activity and amino acid metabolism. • The abundance of g_Acinetobacter was positiv...