As the development of knowledge economic, this research investigates the issue of taxation of e-commerce. In an e-commerce economic environment in which is dominated by productions, sales and consumption of non-physical products rather than traditional physical products, this study is further analyzed by using Delphi Method and Analytical Hierarchy Process. Topics concerning the legitimation and execution of taxation associated with e-commerce transaction, the legitimacy of current law and the mechanism of taxation are examined in this research. The author provides evidence to support the conclusion that e-commerce business is supposed to pay its commercial tax and income tax. Additionally, consisting with the transaction mode of e-commerce and the digitization of paying tax, taxation levying and auditing are suggested to be consequently re-constructed.