PURPOSE: To investigate longitudinal changes in the retinal and choroidal microstructure of the macula in patients with retinitis pigmentosa (RP). DESIGN: Retrospective, observational cohort study. METHODS: A total of 69 patients with RP and 69 age- and sex-matched controls who underwent optical coherence tomography (OCT) over a 4-year follow-up period were included. The severity of RP was classified into 3 stages according to the integrity of the inner segment ellipsoid zone. The retinal and choroidal layers were segmented manually from OCT images. The areas of retinal pigment epithelium (RPE) atrophy and choroidal vascular index (CVI) were also analyzed. Longitudinal changes in the OCT parameters were compared among the groups. RESULTS: Significant decreases (median [interquartile range]) in the thickness of the ganglion cell inner plexiform layer (GCIPL; −1.04 [−2.41 to −0.17]), outer nuclear layer (ONL; −1.44 [−1.86 to −0.28]), and inner segment ellipsoid (ISE; −0.74 [−1.33 to −0.49]) at the moderate stage and retinal nerve fiber layer (RNFL; −1.49 [−2.08 to −0.66]) and GCIPL (0.58 [−1.79 to 0.06]) at the advanced stage were observed. Choroidal thickness decreased significantly from −7.62 to −9.40 μm per year at all stages. RPE atrophy and CVI reduction were observed at the advanced stage. There was no change in the control group. CONCLUSIONS: ONL and GCIPL thicknesses decreased at the moderate and advanced stages of RP; RNFL thickness decreased only at the advanced stage; and choroidal thickness decreased continuously. In addition, RPE atrophy and CVI reduction were prominent at the advanced stage. These results indicate that there is a temporal variation in the damage of each retinal layer and the choroid in RP patients.