Abstract: Objective To determinate small molecules in elderly patients with malnutrition plasma metabolic substances by using GC-MS method, looking for is closely related to the malnutrition in elderly patients with development of small molecule metabolites; to discuss application of metabonomics in elderly patients with malnutrition. Methods From February, 2015 to February, 2016 in our hospital diagnosis and treatment of 30 cases of malnutrition in elderly patients were selected as experimental group, during the same period by age, gender, match the old people in 30 cases of normal nutritional status as the control group. Acquisition of both groups respectively since morning fasting venous blood 5 ml, let stand separation blood plasma, repackaging kept at low temperature. The two groups was evaluated by GC-MS method plasma small molecule metabolic substances. Using principal component analysis and discriminant analysis on two groups of minimum variance research object plasma statistical analysis of small molecules metabolic substances small molecules and compare the two groups of plasma metabolic material level. Results Both groups blood plasma total ion current chromatogram basic similar. The chromatographic retention time are mainly concentrated in 5-15 min, The experimental group was significantly lower than the control group. The experimental way and the control sample principal component score chart can clearly distinguish. The experimental group and control group permutation test intercept R²=0.668, Q²=0.309. glycine, aspartic acid. Sue sugar acid response values of the experimental group were higher than the control group, while ornithine, oleic acid, uric acid, D-talose, N-methyl-DL-alanine, mannose, D-glycerophosphate, alpha and beta alanine glutaric response values to lower (P<0.05). Conclusion GC-MS method can detect small molecules related to the elderly patients with malnutrition metabolic material types, Prompt GC-MS method can be used as in elderly patients with malnutrition screening of small molecule metabolites detection method.