A novel method of cell affinity screening (CAS), cell affinity capture coupled with LC-MS analysis, was developed for screening the bioactive compounds related to cardiovascular diseases from the natural product libraries. One of the major characteristics lies in its function in affinity-capturing and separating the bioactive components from the natural product libraries in vitro. Another characteristic is its use in analyzing and identifying the target compounds, by employing high-performance liquid chromatography and mass spectrometry. CAS was used for screening the bioactive components from the alkaloid extract derived from Aconitum szechenyianum Gay. Of the five components found to be bound to the oxidative-damaged endothelial cells, the two compounds identified, mesaconitine and aconitine, were recognized in the literature as being related to cardiovascular diseases.