Nitrogen-containing compounds especially alkaloids are important medicinal ingredients in caulis dendrobii plants. Using solid-phase extraction coupled with liquid chromatography tandem mass spectrometry and multivariate data analysis methods, metabolic profiling of the nitrogen-containing compounds was established to distinguish Dendrobium huoshanense and Dendrobium officinale. Hundreds of nitrogen-containing compounds from the two caulis dendrobii were purified by the MCX cartridges. Some compounds were identified by high-resolution tandem mass spectrometry technology. Together with multivariate data analysis methods, comparative analysis of the metabolic profiling from two caulis dendrobii was conducted. A total of 133 nitrogen-containing compounds were identified, including amino acids, pyrrolidines, tropanes, pyrimidines, purines, indoles, piperidines, guanidines, quinolines, isoquinolines and terpenoids. Metabolic profiling analysis showed that the composition and contents of these chemical components were significantly different between D. huoshanense and D. officinale. Moreover, some components were species-specific, distributed in the two caulis dendrobii, such as pilosine, ternatusine, etc. Because alkaloids are mainly derived from amino acids via multistep biochemical reactions, the correlation analysis suggested that amino acids were partially associated with several types of components and significantly correlated with certain alkaloids. Arginine was extremely correlated with guanidines. Pyrimidines, purines and niacin-nicotinamide metabolic intermediates were associated with three independent networks. The results further enriched the chemical components currently identified from caulis dendrobii and provided a technical reference for detecting nitrogen-containing compounds in other medicinal plants. © 2020, Prof. H.S. Srivastava Foundation for Science and Society.