In this study, habitat differentiation and degradation characterization of Cinnamomi Cortex (CC) were carried out using 1H NMR spectroscopy coupled with multivariate statistical analysis. Twenty-one components were plausibly identified in 1H NMR spectrum of CC, among which fatty acid, β-glucose, cinnamaldehyde and other seven compounds were screened out as reasonable chemical markers in orthogonal partial least squares-discriminant analysis (OPLS-DA), being responsible for the habitat discrimination of CC from Guangdong and Guangxi provinces of China. The results of 1H NMR spectroscopy combined with principal component analysis (PCA) revealed that the contents of coumarin and carbohydrates changed mildly during two week-storage, while the degradation of cinnamaldehyde along with some fatty acids was crucial. The degradated products of cinnamaldehyde were supposed as cinnamic acid and styrene, the latter of which is a potential neurotoxic and hepatotoxic compound. The results of radical scavenging assays suggested that degradation could down-regulate anti-oxidation performance of CC. Thus, the efficacy and safety of CC extract after long time storage deserve attention. Above all, 1H NMR spectroscopy can be used as a reliable tool to assess the quality of medicinal herbs as well as herbal dietary supplements.