Macrobiomolecular treatments for ocular inflammatory diseases have been described in a previous review. This article mainly discusses the application of small molecules in uveitis therapy, which includes corticosteroids, salicylic acid (aspirin), metabolite analogs, and anti-oxidative agents. Additionally, we update recent advances in peptide and nucleic acid related therapies, and focus mainly on the calcineurin inhibitor, cyclosporine, oral tolerant retinal proteins/peptides, gene therapy and ribonucleic acid interference strategies. We classify these immunomodulatory agents by their molecular signatures and highlight the molecular structure and mechanisms of function. These developments in understanding molecular mechanisms of the diseases, with the advent of new technologies, advance current therapeutic approaches. The future direction is to tailor treatments to individual patients in order to provide the safest and most effective therapies for ocular inflammatory diseases.