Abstract Background Along with an aging society, the global burden of heart failure (HF) is evident in Japan. Recent reports showed that malnutrition is one of the frequent comorbidity in patients with HF, and this grievous issue is related to worsening prognosis in such subjects. There are many screening tools of nutrition risks, however, feasible indexes or strategies for evaluating nutrition risk in patients with HF remain to be identified definitively. Purpose The purpose of the present study was to examine the effectiveness of various nutrition indexes on 3-year mortality in hospitalized acute HF patients. Methods The study population comprised a total of 817 individuals who were hospitalized for acute HF between November 2009 and December 2015, and was followed up for 3 years. All the previously established objective nutritional indexes [The controlling nutritional status (CONUT) score, geriatric nutritional risk index (GNRI), and subjective global assessment (SGA)] were evaluated at the time of hospital admission. Malnutrition status of each index was defined as CONUT score ≥5, GNRI <91, or SGA (B and C), respectively. We evaluated combined predictive values of these indexes for 3-year mortality by Cox regression model, and calculated the net reclassification improvement (NRI) and the integrated discrimination improvement (IDI). Results The median age was 79 (interquartile range 70–85) years, and 55.7% of the subjects were male. The frequency of malnutrition was 18.1% in CONUT score, 31.9% in GNRI, and 25.9% in SGA. The rate of 3-year mortality was 32.2%. All indexes were related to the occurrence of 3-year mortality by univariate analyses (P<0.001). We examined combined predictive values by calculating multivariable-adjusted hazard ratios (aHR) and 95% confidence intervals (CI) for associations of malnutrition by these 3 indexes and prognostic variables identified by multivariable Cox regression model (age, body mass index, systolic blood pressure, reduced eGFR, albumin, and prior HF hospitalization). Malnutrition of all 3 indexes (5.6% of the subjects) was associated with higher relative risk of 3-year mortality than well-nutrition (aHR 1.90; 95% CI 1.07–3.35, P=0.028), or malnutrition of any 1 index (aHR 1.95; 95% CI 1.18–3.21, P=0.009). Next, we individually included each value into a reference model (age, body mass index, reduced eGFR, albumin, prior HF hospitalization, and ischemic etiology by multivariable logistic regression analysis with P<0.05). SGA was superior according to comprehensive discrimination, calibration, and reclassification analysis (NRI 0.212, P=0.003; IDI 0.005, P=0.029). Similar analysis with other indexes (CONUT score or GNRI) revealed no improvement. Conclusion Our present results suggest that simultaneous addition of CONUT, GNRI, and SGA seems useful for predicting long-term mortality in acute HF. In addition, nutritional screening with SGA independently improves mortality risk stratification.