Malnutrition is a risk factor for disease progression and poor prognosis in chronic kidney disease (CKD). However, the complexity of nutritional status assessment limits its clinical application. This study explored a new method of nutritional assessment in CKD (stage 1–5) patients using the Subjective Global Assessment (SGA) as the gold standard and evaluated its applicability. The kappa test was used to analyze the consistency of the Renal Inpatient Nutrition Screening Tool (Renal iNUT) with SGA and protein-energy wasting. Logistic regression analysis was used to analyze the risk factors of CKD malnutrition and calculate the prediction probability of multiple indicators combined for the diagnosis of CKD malnutrition. The receiver operating characteristic curve of the prediction probability was drawn to evaluate its diagnostic efficiency. A total of 161 CKD patients were included in this study. The prevalence of malnutrition according to SGA was 19.9%. The results showed that Renal iNUT had a moderate consistency with SGA and a general consistency with protein-energy wasting. Age > 60 years (odds ratio, OR = 6.78), neutrophil–lymphocyte ratio > 2.62 (OR = 3.862), transferrin < 200 mg/dL (OR = 4.222), phase angle < 4.5° (OR = 7.478), and body fat percentage < 10% (OR = 19.119) were risk factors for malnutrition in patients with CKD. The area under the receiver operating characteristic curve of multiple indicators for the diagnosis of CKD malnutrition was 0.89 (95% confidence interval: 0.834–0.946,p< 0.001). This study demonstrated that Renal iNUT has good specificity as a new tool for the nutrition screening of CKD patients, but its sensitivity needs to be optimized. Advanced age, high neutrophil–lymphocyte ratio, low transferrin level, low phase angle, and low body fat percentage are risk factors for malnutrition in patients with CKD. The combination of the above indicators has high diagnostic efficiency in the diagnosis of CKD malnutrition, which may be an objective, simple, and reliable method to evaluate the nutritional status of patients with CKD.