This study aimed to evaluate the effect of Datura stramonium on rats by examining the differences in urine and serum metabolites between Datura stramonium groups and control group. SIMCA-P+12.0.1.0 software was used for partial least-squares discriminant analysis (PLS-DA) to screen for the differential metabolites. Fifteen metabolites in urine including malonic acid, pentanedioic acid, D-xylose, D-ribose, xylulose, azelaic acid, threitol, glycine, butanoic acid, D-mannose, D-gluconic acid, galactonic acid, myo-inositol, octadecanoic acid, pseudouridine and ten metabolites in serum including alanine, butanedioic acid, L-methionine, propanedioic acid, hexadecanoic acid, D-fructose, tetradecanoic acid, D-glucose, D-galactose, oleic acid were selected as the characteristic metabolites. The PLS-DA scores plot indicated that serum and urine metabolites have a variety of changes among low dose group, high dose group and control group. These metabolites were related with amino metabolism, lipid metabolism and energy metabolism. The result reflected the relationship between metabolites in rat fluid and Datura stramonium spectra. Potential differences in metabolites and metabolic pathway analysis showed that the establishment of urine and serum metabolomics methods for further evaluating drug has great significance.