Purpose: To investigate longitudinal changes in peripapillary choroidal thickness (pCT) and retinal nerve fiber thickness (pRNFLT) in patients with Type 2 diabetes mellitus.Methods: This was a prospective observational cohort study. Patients with Type 2 diabetes mellitus without diabetic retinopathy (DR) at baseline were recruited, followed up for three years, and further divided into an incident DR group and a non-DR group according to the outcome. The pCT and pRNFLT were measured through swept-source optical coherence tomography at 1-year interval, and the mean rates of pCT and pRNFLT thinning were compared between the DR groups.Results: A total of 682 patients (682 eyes) were included in the final analysis. After 3years follow-up, 122 (17.89%) developed DR. Both pCT and pRNFLT progressively thinned (22.37 [22.80 to 21.95] mm/year; 20.40 [20.55 to 20.25] mm/year, respectively, P , 0.05) and accelerated thinning was observed in the incident DR group. The rates of pCT thinning (23.92 [24.96 to 22.88] mm/year, 22.03 [22.49 to 21.57] mm/year, respectively) and pRNFLT loss (21.03 [21.31 to 20.76] mm/year, 20.26 [20.43 to 20.09] mm/year, respectively) in the incident DR group were 1.93 and 3.96 times faster than those in the non-DR group, respectively. In addition, pCT and pRNFLT thinning were negatively related in Type 2 diabetes mellitus population, and faster pCT thinning indicated slower pRNFLT loss.Conclusion: Patients with Type 2 diabetes mellitus were at a higher risk of developing DR when accelerated pCT and pRNFLT thinning were present, indicating that heavier choroidal damage and retinal neurodegeneration precede clinical DR. The pCT and pRNFLT have the potential to serve as novel sensitive biomarkers of preclinical and early DR.