Ocular irritation and tear-film instability are common among school-aged children, yet the microbial and chemical features of classroom dust associated with these outcomes remain poorly characterized. We conducted a cross-sectional multi-omics study in 32 classrooms from eight Indonesian junior high schools, integrating shotgun metagenomics and untargeted LC-MS metabolomics of settled dust with ocular symptoms and tear film break-up time (TFBUT) from 380 students. Classrooms with a low prevalence of ocular irritation were enriched in Actinobacteriota such as Allosaccharopolyspora coralli, Saccharopolyspora dendranthemae, and Brevibacterium epidermidis (LDA > 2, P 2, P