Protein biomarkers from plasma extracellular vesicles (EVs) have been extensively identified in various diseases. To explore biomarkers associated with diabetic retinopathy (DR) progression, we designed two cohorts, discovery and validation cohorts, including four groups: healthy control, type 2 diabetes mellitus, non-proliferative DR (NPDR), and proliferative DR (PDR). A total of 32 differentially expressed proteins (DEPs) were screened by proteomic analysis in the four groups of the discovery cohort. Among them, four hub proteins, CELA3A, CELA3B, GLUD1, and CTRC, were identified to be related to DR progression, and their correlation with clinical characteristics was further analyzed. Subsequently, enzyme-linked immunosorbent assay in the validation cohort confirmed that the expression levels of CELA3A, CELA3B, and CTRC were consistent with the proteomic results. Receiver operator characteristic curve analysis found that the AUC values of three hub proteins and their composed panels distinguishing NPDR/PDR from DM were all > 0.7, except for DM-NPDR of CELA3B. In addition, CELA3A, CELA3B, and CTRC proteins were significantly correlated with some clinical indicators of DR. This study indicates that the plasma EV proteins CELA3A, CELA3B, and CTRC are expected to become biomarkers to monitor DR progression and provide guidance for DR diagnosis.