Objective To investigate the application of metabolomics in research of the metabolic profiling of spontaneously hypertensive rats (SHR) and Wistar rats using NMR combined with PLS-DA. Methods SHRs were fed with normal diet for 1 week and then the urines of normal rats and SHR hypertensive model rats were collected at 1, 2, 3, and 4 weeks. The metabolic profiles were analyzed using ¹H-NMR. Partial least squares discriminant analysis (PLS-DA) was used to determine the differential biomarkers. Results The systolic blood pressure (SBP) of SHRs were significantly higher than that of normal rats. Using PLS-DA and orthogonal partial least squares discriminant analysis (OPLS-DA), it was also possible to distinguish them in the principal components score plot. In the SHRs, the levels of some amino acids and some small molecular substances were higher than those in the control rats. Conclusions NMR combined with PLS-DA is a promising approach to provide the information on metabolic changes related to the pathophysiological processes in spontaneously hypertensive rats.