3-(4-Chlorophenyl)-7-[2-(piperazin-1-yl)ethoxy]-4H-chromen-4-one (CPEO-43) is a derivative of soybean isoflavone (SI), synthesized by introducing a chlorine atom and a piperazine group into the structure of natural SI. In vitro experiments have demonstrated that CPEO-43 exhibits a notable inhibitory effect on both A549 cells and HCT116 cells. For the further development and utilization of CPEO-43, this study aims to establish and validate a liquid chromatography-tandem mass spectrometry (LC-MS/MS) quantitative analysis method for the pharmacokinetic study of CPEO-43. Normal rats were intragastrically administered different doses (2, 6, and 20 mg/kg) of CPEO-43, and blood was taken from the ocular venous plexus at different time points. The blood concentration of CPEO-43 at different time points was determined using LC-MS/MS technology, and the pharmacokinetic parameters of the compound were calculated using the pharmacokinetic software DAS. The results indicated that the established LC-MS/MS method complies with the standards for bioanalytical method validation in the Chinese Pharmacopoeia (CHP) and can be applied to the pharmacokinetic study of CPEO-43. The pharmacokinetic software DAS non-compartmental model was successfully used to calculate the Cmax, Tmax, t1/2, AUC0–∞, MRTs, CL, and Vd pharmacokinetic parameters of the compound at different doses. The results were as follows: 62.0 ± 10.5, 222.0 ± 28.7, and 1384.5 ± 376.4 ng/mL; 8.5 ± 1.2, 6.0 ± 0.0, and 11.0 ± 6.2 h; 15.6, 15.0, and 18.5 h; 1517.8 ± 317.0, 5328.7 ± 864.4, and 45556.3 ± 22735.6 ng·h/mL; 17.8 ± 1.2, 17.7 ± 0.8, and 20.0 ± 3.2 h; 1370.3 ± 305.9, 1153.5 ± 205.6, and 505.3 ± 179.8 mL/kg/h; 30843.0 ± 7458.0, 24344.0 ± 5237.0, and 13950.3 ± 5996.9 mL/kg. These characteristics are of great significance for understanding the in vivo process of the drug, formulating dosing regimens, and evaluating the safety and efficacy of the drug.