The aim of this study was to investigate associations between age-dependent variations in isolated systolic/diastolic hypertension (ISH/IDH) with target organ damage in chronic kidney disease (CKD). A cross-sectional study was conducted among 2,459 CKD patients with ambulatory blood pressure monitoring. Blood pressure was categorized into four groups: normotension, ISH, IDH, and systolic-diastolic hypertension. The outcome measurements were left ventricular mass index (LVMI), estimated glomerular filtration rate(eGFR), and urinary albumin creatinine ratio (ACR). Older patients (≥60-years-old) had a higher prevalence of ISH and a lower prevalence of IDH than younger patients (<60-years-old). In multivariate analysis, compared with the normotension group, younger patients with ISH were associated with higher LVMI (+14.4 g/m2), lower eGFR (−0.2 log units), and higher ACR (+0.5 log units); but younger patients with IDH were only associated with lower eGFR (−0.2 log units) and higher ACR (+0.4 log units). Among older patients, ISH was correlated with higher LVMI (+8.8 g/m2), lower eGFR (−0.2 log units), and higher ACR (+1.0 log units), whereas IDH was not associated with these renal/cardiovascular parameters. In conclusion, ISH was associated with a relatively high risk of target organ damage irrespective of age, whereas IDH was only correlated with renal injury in younger CKD patients.