To study the effect of different processes of Crotonis Fructus on fatty oil, total protein and intestinal toxicity, three kinds of processed products (heat Crotonis Semen Pulveratum, non-heat Crotonis Semen Pulveratum and diluted Crotonis Semen Pulveratum) were prepared. Mice were orally given Crotonis Fructus. The content of DAO and D-lactic acid in the serum were measured by ELISA to investigate the change of intestinal permeability in mice. Western blot was used to determine the expressions of tight junction proteins (occludin, claudin-1) in different intestinal tract, so as to observe the effect of Crotonis Fructus and its processed products on intestinal epithelial barrier. These results showed that Crotonis Fructus could significantly increase the intestinal permeability and reduce the expression of tight junction proteins in duodenum and jejunum, but with little impact on the ileum and colon. The intestinal permeability and the expression of tight junction proteins became normal after processing. However, the order of the toxicity of Crotonis Semen Pulveratum from high to low was non-heat Crotonis Semen Pulveratum > diluted Crotonis Semen Pulveratum≈4heat Crotonis Semen Pulveratum. According to the results of composition, the composition of fatty oil did not change during the processing, but the content and composition of total protein in Crotonis Semen Pulveratum changed significantly. The order of total protein content from high to low was that non-heat Crotonis Semen Pulveratum > heat Crotonis Semen Pulveratum > diluted Crotonis Semen Pulveratum. The molecular weight distribution of the total protein bands of non-heat Crotonis Semen Pulveratum and diluted Crotonis Semen Pulveratum was consistent, but the composition of total protein of heat Crotonis Semen Pulveratum significantly changed as evidenced by decreased and thin some stripes. This indicated that heating and dilution could reduce the content of total protein, and heating could cause partial protein denaturation and inactivation. In conclusion, both dilution and heating can reduce the toxicity of Crotonis Fructus, but the heating shows a more significant attenuation effect, indicating that heating is the key step in Crotonis Semen Pulveratum preparation.