Background: Malnutrition and inflammation are highly prevalent and tightly regulated with each other in chronic kidney disease (CKD) patients. Inflammation can lead to malnutrition in patients with sufficient nourishment, while malnutrition may also induce an inflammatory response. This study investigated whether the albumin-globulin ratio (AGR) can predict the mortality risk in CKD patients. Methods: We enrolled 956 stage 3–5 CKD patients retrospectively at a medical center. Patients’ baseline characteristics including demographics, laboratory data, pharmacotherapy, and comorbidities were collected for statistical adjustments. The study patients were stratified into three AGR groups according to similar magnitudes of hazards for mortality as follows: low AGR group, AGR ≤ 1.0; moderate AGR group, 1.1 ≤ AGR < 1.3; high AGR group, AGR ≥1.3. Multivariate Cox proportional hazard analysis was performed to evaluate the association of the AGR with the study outcomes, including overall and cardiovascular disease (CVD) mortality. Results: During a median follow-up duration of 2.44 years, 108 (11.3%) deaths were recorded and 50 patients died from CVD. In adjusted model 1, the moderate AGR group was associated with hazard ratios (HR) of 0.57 (95% CI = 0.36–0.90, p = 0.016) and 0.52 (95% CI = 0.28–0.98, p = 0.043) for all-cause and CVD mortality compared with the low AGR group, respectively. The high AGR group was associated with HRs of 0.49 (95% CI = 0.27–0.90, p = 0.021) and 0.27 (95% CI = 0.1–0.74, p = 0.01) for all-cause and CVD mortality compared with the low AGR group, respectively. Similar results were obtained in the adjusted model 2 (inverse probability of the group weighted Cox model). In addition, the association between the AGR and mortality risk remained significant when the AGR was treated as a continuous variable. Conclusion: AGR is a significant biomarker predicting overall and cardiovascular mortality risk independent of various important factors amongst stage 3–5 CKD patients. We suggest that the AGR may be a simple and inexpensive measurement for detecting CKD patients at risk of mortality.