Chronic kidney disease (CKD) is an emerging disease worldwide. We investigated the relationship between blood pressure (BP) control and parafoveal retinal microvascular changes in patients with CKD. This case-control study enrolled 256 patients with CKD (stage 3-5) and 70 age-matched healthy controls. Optical coherence tomography angiography showed lower superficial vascular plexus (SVP) vessel density, lower deep vascular plexus (DVP) vessel density, and larger SVP flow void area in the CKD group. The BP parameters at enrollment and during the year before enrollment were collected in patients with CKD. Partial correlation was used to determine the relationship between BP parameters and microvascular parameters after controlling for age, sex, diabetes mellitus, axial length, and intraocular pressure. The maximum systolic blood pressure (SBP) (p = 0.003) and within-patient standard deviation (SD) of SBP (p = 0.006) in 1 year were negatively correlated with SVP vessel density. The average SBP (p = 0.040), maximum SBP (p = 0.001), within-patient SD of SBP (p < 0.001) and proportion of high BP measurement (p = 0.011) in 1 year were positively correlated with the SVP flow void area. We concluded that long-term SBP was correlated with SVP microvascular injury in patients with CKD. Superficial retinal microvascular changes may be a potential biomarker for prior long-term BP control in these patients.