Fine particulate matter (PM2.5) is known to exacerbate chronic respiratory disorders, primarily by inducing inflammatory responses and mucus overproduction. Perilla leaves are reported to have significant health benefits, such as antioxidant, antibacterial, and antiallergic properties, attributed to phenolic compounds that vary depending on genetic diversity. In this study, flavonoid‐rich extracts (FRE) from 56 perilla leaf varieties and genetic resources were prepared and screened using a mass screening system. The screening focused on evaluating their anti‐inflammatory, mucus‐reducing, and respiratory protective effects against PM2.5‐induced damage in human nasal cells (RPMI2650). Parameters such as cell viability, nitric oxide (NO) levels, and mucus secretion factor (MUC5AC) concentrations were assessed. Among the 56 varieties, Perilla frutescens var. crispa (YCPL706), sourced from Ulleung Island, Korea, exhibited the highest cell viability (112.50%, 100 μg/mL), lowest NO concentration (9.98 μM, 100 μg/mL), and MUC5AC level (78.65 ng/mL, 100 μg/mL). Further evaluation of YCPL706 FRE demonstrated significant respiratory protective effects, including the inhibition of pro‐inflammatory cytokines (TNF‐α, IL‐6, and IL‐1β), MUC5AC, and oxidative stress factors (MDA and ROS), compared to the control cultivar Namcheon. YCPL706 also showed strong antibacterial activity against Pseudomonas aeruginosa (minimum inhibitory concentration: 5 mg/mL). These findings suggest that the genetic resource YCPL706 is a promising candidate for combating PM2.5‐induced respiratory damage due to its potent anti‐inflammatory, antioxidant, and antibacterial properties.