Malnutrition and acute kidney injury (AKI) are common complications in hospitalized patients, and both increase mortality; however, the relationship between them is unknown. This is a retrospective propensity score matching study enrolling 46,549 inpatients, aimed to investigate the association between Nutritional Risk Screening 2002 (NRS-2002) and AKI, and to assess the ability of NRS-2002 and AKI in predicting prognosis. In total, 37,190 (80%) and 9,359 (20%) patients had NRS-2002 scores < 3 and ≥ 3, respectively. Patients with NRS-2002 scores ≥ 3 had longer lengths of stay (12.6±7.8 days vs. 10.4±6.2 days, P < 0.05), higher mortality rates (9.6% vs. 2.5%, P<0.05), and higher incidence of AKI (28% vs. 16%, P < 0.05) than normal nutritional patients. The NRS-2002 showed a strong association with AKI, that is, the risk of AKI changed in parallel with the score of the NRS-2002. In short- and long-term survival, patients with a lower NRS-2002 score or who did not have AKI achieved a significantly lower risk of mortality than those with a high NRS-2002 score or AKI. Univariate Cox regression analyses indicated that both the NRS-2002 and AKI were strongly related to long-term survival (area under the curve (AUC) 0.79 and 0.71) and that the combination of the two showed better accuracy (AUC 0.80) than the individual variables. In conclusion, malnutrition can increase the risk of AKI, and both AKI and malnutrition can worsen the prognosis, that the undernourished patients who develop AKI yield far worse prognosis than normal nutritional patients.