Kudouzi (Sophora alopecuroides L., Fabaceae) is an effective folk medicine, but it always causes a hepatic and renal toxicity in clinical therapy. The toxic mechanism remains unclear. This paper detected the urinary and plasma metabolites alteration by 1H NMR-based metabonomics study in Kudouzi-induced rats to evaluate the toxic mechanism for clinical security. The male Sprague-Dawley rats were orally dosed with 0.5 and 1 g Kudouzi/kg weight once per day for consecutive 14 days. Urine samples were collected at day −1 (before treatment), and days 7, 14, and 21 for NMR analysis, respectively. Plasma samples were harvested at day 14 for NMR and biochemical analysis. The metabonomic profiling of Kudouzi-treated rats differed from that of the vehicle. This was confirmed by the biochemistry analysis. The accumulated subacute toxicity of Kudouzi was visible with dosing time, and persisted at day 21 even after the disposal was ended. The observable biochemical pathways alterations included inhibited TCA cycle, activated anaerobic glycolysis, perturbed amino acids metabolism, and disordered gut microbiota. The results evidenced the toxicity mechanism of Kudouzi from a systematic and holistic view.