Objective: To compare the effect of processing on naphthopyrone glycosides and anthraquinone aglycones in Semen Cassiae. Method: The high-performance liquid chromatographic method was used to determine the content of three naphthopyrone glycosides and three anthraquinone aglycones in Semen Cassiae and compare the changes in the content before and after processing. Result: The content of three naphthopyrone glycosides significantly decreased after processing. Specifically, rubrofusaringentiobioside dropped about 21%, cassiaside decreased by 60%, cassiaside C decreased by 87%. As for the changes in the content of the three anthraquinones, there was no significant difference between aurantio-obtusin and chryso-obtusin, but obtusifolin increased by 48%. Conclusion: Processing has a significant effect on the content of naphthopyrone glycosides and anthraquinone aglycones in Semen Cassiae. Specifically, naphthopyrone glycosides in Semen Cassiae decreased integrally, whole anthraquinone aglycones increased partially after processing.