Radiation pneumonitis (RP) is a dose-limiting complication of thoracic radiotherapy, and effective preventive interventions remain limited. Lycium ruthenicum anthocyanins (LRACN) exhibit antioxidant and anti-inflammatory activities, but their effects on RP and the associated systemic mechanisms remain unclear. In this study, a mouse RP model was established by 15 Gy localised chest irradiation, and LRACN was administered orally before and after irradiation. Protective effects were evaluated using histopathology, inflammatory cytokines, and oxidative stress indices. Potential mechanisms were explored by integrating 16S rRNA sequencing, non-targeted serum metabolomics, metabolite-based target network analysis, transcriptomics, and single-cell RNA-seq. Compared with the model group, high-dose LRACN reduced injury score, collagen volume fraction, tumour necrosis factor-α, and malondialdehyde in the lung tissue by approximately 55%, 58%, 45%, and 44%, respectively. Multi-omics profiling revealed that LRACN partially restored radiation-disrupted gut microbial taxa, including Dubosiella, Ligilactobacillus, and Akkermansia, and reversed radiation-induced disturbances in serum purine and glycerophospholipid metabolism. Correlation analysis linked LRACN-responsive gut taxa and circulating metabolites with RP-related pathological, inflammatory, and oxidative indices. Integrated pathway analysis and western blotting suggested that the protective effect of LRACN was associated with reduced PI3K and Akt phosphorylation in lung tissue. These findings indicate that LRACN mitigates early RP in mice, and gut microbiota-associated metabolic remodelling may contribute to its protective effects.