This study aimed to investigate whether a combined estimation of the geriatric nutritional risk index (GNRI) and the modified creatinine index (mCI) provides synergistic information for mortality in patients treated by chronic hemodialysis. We analyzed 499 patients on hemodialysis for five years. We set each cut-off value as the high (≥92) and low (<92) GNRI groups and the high (≥21 mg/kg/day) and low (<21 mg/kg/day) mCI groups, and divided them into four subgroups: G1, high GNRI + high mCI; G2, high GNRI + low mCI; G3, low GNRI + high mCI; and G4, low GNRI + low mCI. The survival rate was evaluated and time-to-event analysis was performed. All-cause death occurred in 142 (28%) patients. Kaplan–Meier curves showed that G2 and G4 had a significantly worse outcome (p < 0.05) than G1 but not G3. Using the multivariable-adjusted model, only G4 was significantly associated with all-cause mortality compared with G1. Our study suggests that the synergistic effects of the GNRI and the mCI are helpful in predicting all-cause mortality. The combination of these indices may be superior to a single method to distinguish patients who are well or moderately ill from potentially severely ill.