The invention discloses a composition for treating eye diseases by double-target / multi-target small nucleic acid and applications of the composition. The composition comprises two small nucleic acid molecules and a medicinal carrier, target genes of the two small nucleic acid molecules are selected from two of VEGF (vascular endothelial growth factor) gene, VEGFR2 (vascular endothelial growth factor receptor2) gene and TGF-b1 (transforming growth factor-beta1) gene; or the composition comprises three small nucleic acid molecules and a medicinal carrier, and target genes of the three small nucleic acid molecules are respectively VEGF gene, VEGFR2 gene and TGF-b1 gene. The composition can be used for effectively treating eye diseases by virtue of ribonucleic acid interference (RNAi) mediated inhibitor gene expression and biochemical pathway, and can be prepared to form a medicament for treating eye diseases, including proliferatived diabetic retinophathy, diabetic macular edema, herpes simplex interstitial keratitis, age-related macular degeneration, uveitis and the like.