Background: The underlying mechanism as well as diagnostic molecular biomarkers for corneal endothelial cell dysfunction (CECD) remain elusive. This study aimed to elucidate molecular mechanism of CECD via proteomic and transcriptomic approaches and identify novel biomarkers in aqueous humor (AH) directly associated with changes in CECs. Methods: We carried out an in-depth proteomic analysis of patient-derived AH as well as transcriptomic analysis of CECs from the same patients with bullous keratopathy (BK) resulting from CECD. Selected candidate proteins were further verified by individual data-independent acquisition and immunoassay using further AH samples from CECD patients. Findings: Using integrated multi-omics analysis, systematic alterations of proteins in AH and mRNA in CECs were mainly associated with the immune mechanism during BK development. Through individual proteomic verification via DIA analysis, three AH proteins were determined as potential predictive markers including TIMP1, FCGBP, and ANGPTL7. Finally, we confirmed these biomarkers using immunoassay in individual AH samples of CECD. Interpretation: Our multi-omics analysis may provide valuable insights into the disease-specific process as well as possibility of biofluid biomarkers in CECD. Further investigation with large scale is required to determine whether AH biomarkers are useful as liquid biopsy targets for the assessment of CEC function