In this study, a new capillary electrophoresis (CE) method was developed for the online determination of platelet aggregation induced by thrombin (THR). The developed CE method was applied to evaluate the anti-platelet aggregation activity of Rhizoma Corydalis extract. Besides, the anti-platelet activity of Rhizoma Corydalis extract was also evaluated by the classic turbidimetry method for comparison. The results showed that platelet aggregation rate could be obtained or calculated based on the peak height or peak area of free platelets in CE analysis, and the anti-platelet aggregation activities of Rhizoma Corydalis extract were both dose-dependent manner determined by the CE and turbidimetry methods. Furthermore, compared with classic turbidimetry for platelet aggregation assay, CE is superior in smaller sample consumption and higher repeatability. Therefore, CE may be a potential method for evaluating anti-platelet aggregation activity of drugs.