AimsTo investigate longitudinal choroid and ganglion cell–inner plexiform layer (GCIPL) changes in type 2 diabetes mellitus (T2DM) patients and healthy populations across 2 years.MethodsThis prospective cohort study included T2DM patients and healthy controls. T2DM patients were divided into mild non-proliferative diabetic retinopathy (NPDR) or non-DR (NDR) groups. Macular choroidal and GCIPL thickness was measured using swept-source optical coherence tomography at baseline and follow-up after 2 years. A linear-mixed effect model compared rates of change in choroidal and GCIPL thicknesses between the three groups.Results895 T2DM patients (770 in the NDR group and 125 in the NPDR group) and 847 healthy controls were included. Following 2 years, choroidal thinning occurred at a rate of −7.7±9.2 µm/year, −8.1±8.7 µm/year and −5.2±8.1 µm/year in NDR, NPDR and control groups, respectively (p<0.001). GCIPL loss occurred quickest in NPDR patients (−0.97±0.97 µm/year), followed by NDR (−0.91±0.89 µm/year) and the control group (−0.04±0.55 µm/year) (p<0.001). Following multivariate adjustment, choroidal thinning was −2.04 µm/year (95% CI: −4.05 to –0.03; p=0.047) and −1.95 µm/year (95% CI: −3.14 to –0.75; p=0.001) faster in NPDR and NDR groups than in the control group, respectively, and GCIPL thinning was −1.02 µm/year (95% CI: −1.19 to –0.84; p<0.001) and −0.88 µm/year (95% CI: −0.98 to –0.78; p<0.001) faster in the NPDR and NDR groups than in the control group, respectively.ConclusionProgressive choroidal and GCIPL thinning occurs in healthy individuals and T2DM patients; however, T2DM undergoes accelerated choroidal and GCIPL loss in NPDR patients.