PurposeThis study aimed to investigate longitudinal changes in choroidal thickness (CT) and ganglion cell-inner plexiform layer thickness (GC-IPLT) across distinct phenotypes of type 2 diabetes mellitus (T2DM) patients. DesignProspective observational cohort study. MethodsT2DM patients were categorized into five groups (SAID, SIDD, SIRD, MOD, and MARD) using K-means clustering based on β-cell function and insulin resistance. Swept-source optical coherence tomography measured baseline and 4-year follow-up CT and GC-IPLT. Linear mixed-effects models assessed absolute and relative changes in CT and GC-IPLT across subtypes. ResultsOver a median 4.11-year follow-up, CT and GC-IPLT decreased significantly across all groups. Choroidal thinning rates were most pronounced in SIDD (-6.5±0.53 µm/year and -3.5±0.24%/year) and SAID (-6.27±0.8 µm/year and -3.19±0.37%/year), while MARD showed the slowest thinning (-3.63±0.34 µm/year and -1.98±0.25%/year). SIRD exhibited the greatest GC-IPLT loss (-0.66±0.05 µm/year and -0.91±0.07%/year), with the least in SIDD (-0.36±0.05 µm/year and -0.49±0.07%/year), all statistically significant (Ps < 0.001). Adjusted for variables, SIDD and SAID groups showed faster CT thinning than MARD [-2.57 µm/year (95% CI: -4.16 to -0.97; P=0.002) and -2.89 µm/year (95% CI: -4.12 to -1.66; P<0.001), respectively]. GC-IPLT thinning was notably accelerated in SIRD versus MARD, but slowed in SIDD relative to MARD [differences of -0.16 µm/year (95% CI: -0.3 to -0.03; P=0.015) and 0.15 µm/year (95% CI: 0.03 to 0.27; P=0.015), respectively]. Stratified analysis revealed significant differences among non-DR groups. ConclusionsMicrovascular damage in the choroid is associated with SIDD patients, whereas early signs of retinal neurodegeneration are evident in SIRD patients. All these changes may precede the onset of DR.