Infectious keratitis is still one of the major causes of visual impairment and blindness, often affecting developing countries. Eye-drop therapy to reduce disease progression is the first line of treatment for infectious keratitis. The current limitations in controlling ophthalmic infections include rapid precorneal drug loss and the inability to provide long-term extraocular drug delivery. The aim of the present study was to develop a novel ophthalmic formulation to treat corneal infection. The formulation was prepared by constructing moxifloxacin (MFX) and dexamethasone (DEX)-loaded nanostructured lipid carriers (Lipo-MFX/DEX) mixed with a collagen/gelatin/alginate (CGA) biodegradable material (CGA-Lipo-MFX/DEX) for prolonged ocular application. The characteristics of the prepared Lipo-MFX/DEX nanoparticles were as follows: average size, 132.1 ± 73.58 nm; zeta potential, -6.27 ± 4.95 mV; entrapment efficiency, 91.5 ± 3.5%; drug content, 18.1 ± 1.7%. Our results indicated that CGA-Lipo-MFX/DEX could release an effective working concentration in 60 min and sustain the drug release for at least 12 h. CGA-Lipo-MFX/DEX did not produce significant toxicities, but it increased cell numbers when co-cultured with ocular epithelial cells. An animal study also confirmed that CGA-Lipo-MFX/DEX could inhibit pathogen microorganism growth and improve corneal wound healing. Our results suggest that CGA-Lipo-MFX/DEX could be a useful anti-inflammatory formulation for ophthalmological disease treatment.