A new term, malnutrition-sarcopenia syndrome (MSS), was recently coined to describe the clinical presentation of both malnutrition and sarcopenia. The aim of this study was to investigate the association between MSS and long-term mortality in older inpatients. We conducted a prospective study in acute geriatric wards of two local hospitals in China. Muscle mass and malnutrition were estimated by anthropometric measures and the Mini Nutritional Assessment (MNA). Of the 453 participants, 14 (3.1%) had sarcopenia with normal nutrition, 139 (30.7%) had malnutrition risk without sarcopenia, 48 (10.6%) had malnutrition risk with sarcopenia, 25 (5.5%) had malnutrition without sarcopenia, and 22 (4.9%) had MSS at baseline. Compared with non-sarcopenic subjects with normal nutrition, subjects with MSS and subjects with malnutrition risk and sarcopenia were more than four times more likely to die (hazard ratio [HR], 4.78; 95% confidence interval [CI], 2.09-10.97; and HR, 4.25; 95% CI, 2.22-8.12, respectively); non-sarcopenic subjects with malnutrition risk were more than two times more likely to die (HR, 2.41; 95% CI, 1.32-4.39). In conclusion, MSS may serve as a prognostic factor in the management of hospitalized older patients.