Objectives: Few studies have examined the association between early diastolic mitral inflow velocity to early diastolic mitral annulus velocity ratio (E/e`) and progression of chronic kidney disease (CKD). Methods: We reviewed the data of 2,238 patients from a large-scale, multicenter, prospective Korean study (2011–2016); 163 patients missing important data including echocardiographic measures were excluded. Renal event was defined as a >50% decrease in estimated glomerular filtration rate (eGFR) from baseline, doubling of serum creatinine, or dialysis initiation. Results: At baseline, the median (interquartile range) ejection fraction (EF) and E/e` were 64.0% (60.0%–68.0%) and 9.1 (7.4–11.9), respectively. The rates of EF <50% and E/e` ≥15 were 1.3% and 9.6%, respectively. The proportion of eGFR <30 ml/min/1.73m2 was 27.2%. During the mean 59.1-month follow-up period, 724 patients (34.9%) experienced renal events. In multivariate Cox proportional hazard regression analysis, the hazard ratio (HR) and 95% confidence interval (CI) per one unit increase in E/e` were 1.027 (1.005–1.050; P = 0.016). In penalized spline curve analysis, the suggested threshold of E/e` for renal events was 12, and the proportion of E/e` ≥12 was 4.1%. The susceptible subgroups for the renal hazard of increased E/e` were patients with EF <64%. Conclusions: Increased E/e` was associated with an increased hazard of renal events, suggesting that diastolic heart dysfunction is a novel risk factor of CKD progression.