To study the transdermal diffusion of baicalin in three Shanghuang Ointment and compare the effect of different skin and ointment bases on diffusion. Methods: Intelligent transdermal test instrument was used to determine the cumulative permeating amounts of baicalin from Shanghuang Carbomer gel（A）, Shanghuang Cream with borneol（B）and without borneol（C）.Then diffusion rate could be calculated. Results: the cumulative permeating amounts and transdermal diffusion rate on mice abdomen skin were significantly higher than those on snake slough（P<0.01）. On snake slough, the cumulative permeating amounts and transdermal diffusion rate of baicalin in cream A was significantly higher than cream B and C（P<0.01，0.01）. The difference of the cumulative permeating amounts between two creams was not significant on mice skin. Conclusion: Different skin will make the different outcome. Shanghuang Carbomer gel can soften cuticles, and snake slough is superior to mice skin because of its high sensitivity, less interferences and excellent stability.