Background: Malnutrition is prevalent in elderly inpatients and is associated with various adverse outcomes during their hospital stay, but the diagnosis of malnutrition still lacks widely applicable criteria. This study aimed to investigate the association of malnutrition diagnosed with the SGA, ESPEN 2015, and GLIM criteria, respectively, with in-hospital complications in elderly patients. Method: Hospitalized patients over 65 years old who had been assessed with the SGA guideline for malnutrition at admission were retrospectively recruited from a large observational cohort study conducted in 34 level-A tertiary hospitals in 18 cities in China from June to September 2014. Malnutrition was then retrospectively diagnosed using the GLIM and ESPEN 2015 criteria, respectively, for comparison with the results of the SGA scale. The risk factors for malnutrition were analyzed using logistic regression, and the value of the three diagnostic criteria in predicting the in-hospital complications was subsequently explored using multivariate regression and the random forest machine learning algorithm. Results: A total of 2526 subjects who met the inclusion and exclusion criteria of the study were selected from the 7122 patients in the dataset, with an average age of 74.63 ± 7.12 years, 59.2% male, and 94.2% married. According to the GLIM, SGA, and ESPEN 2015 criteria, the detection rates of malnutrition were 37.8% (956 subjects), 32.8% (829 subjects), and 17.0% (429 subjects), respectively. The diagnostic consistency between the GLIM and the SGA criteria is better than that between the ESPEN 2015 and the SGA criteria (Kappa statistics, 0.890 vs. 0.590). Logistic regression showed that the risk of developing complications in the GLIM-defined malnutrition patients is 2.414 times higher than that of normal patients, higher than those of the ESPEN 2015 and SGA criteria (1.745 and 1.786 times, respectively). The random forest classifications show that the GLIM criteria have a higher ability to predict complications in these elderly patients than the SGA and ESPEN 2015 criteria with a mean decrease in accuracy of 12.929, 10.251, and 5.819, respectively, and a mean decrease in Gini of 2.055, 1.817, and 1.614, respectively. Conclusion: The prevalence of malnutrition diagnosed with the GLIM criteria is higher than that of the SGA and the ESPEN 2015 criteria. The GLIM criteria are better than the SGA and the ESPEN 2015 criteria for predicting in-hospital complications in elderly patients.