Background: Glaucoma is the leading cause of irreversible blindness worldwide. The molecular etiology of glaucoma is complex and unclear. At present, there are few drugs available for glaucoma treatment. The aim of the present study was to perform a systematic analysis of glaucoma candidate drugs/chemicals based on glaucoma genes including genetic factors and differentially expressed (DE) genes. Methods and Findings: Online Mendelian Inheritance in Man (OMIM), Genome-wide association study (GWAS) Catalog and Phenolyzer databases were used to identify genetic factors associated with glaucoma. GEO was used to identify glaucomarelated RNA datasets. DE genes were identified using the WGCNA R package. The Database for Annotation, Visualization and Integrated Discovery (DAVID), a functional annotation bioinformatics resource, was used to analyze possible signaling pathways for glaucoma genes. The Phenome-wide Association Studies (PheWAS) database was employed to identify the disease spectrum of glaucoma genes. DGIdb, CLUE, and KEGG databases were used to mine drugs targeting glaucoma genes. In total, 401 genes from the genetic databases and 2,068 genes from the DE gene analysis were included in further analysis. In terms of glaucoma-related genetic factors, 54 pathways were significantly enriched (FDR < 0.05) and 96 pathways for DE genes were significantly enriched (FDR < 0.05). A search of the PheWAS database for diseases associated with glaucoma-related gene returned 1,289 diseases, and a search for diseases associated with DE glaucomarelated genes returned 1,356 diseases. Cardiovascular diseases, neurodegenerative diseases, cancer, and ophthalmic diseases were highly related to glaucoma genes. A search of the DGIdb, KEGG, and CLUE databases revealed a set of drugs/chemicals targeting glaucoma genes. A subsequent analysis of the electronic medical records (EMRs) of 136,128 patients treated in Sichuan Provincial People's Hospital for candidate drug usage and the onset of glaucoma revealed nine candidate drugs. Among these drugs, individuals treated with nicardipine had the lowest incidence of glaucoma. Taken together with the information from the drug databases, 40 most likely candidate drugs for glaucoma treatment were highlighted. Conclusions: Based on the findings, we concluded that the molecular mechanism of glaucoma is complex and it may be a reflection of systemic diseases. A set of ready-for-use candidate drugs targeted glaucoma genes, which may be developed for glaucoma clinical treatment drugs. Our results provide a systematic interpretation of glaucoma genes, interactions with other systemic diseases, and candidate drugs/chemicals. Funding Statement: This research project was supported by: the National Natural Science Foundation of China (81670895 (L.H.) and 81300802 (L.H.); the Department of Science and Technology of Sichuan Province, China (2017JQ0024 (L.H.), 2016HH0072 (L.H.), 2015JQO057 (L.H.) and 2013JY0195 (L.H.) Declaration of Interests: The authors declare no competing financial interests. Ethics Approval Statement: The study was approved by the institutional ethics committee of Sichuan Provincial People’s Hospital and was conducted according to the Declaration of Helsinki principles.