The evolution of internet technology has provided a new initiative in electronic commerce or known as e-commerce. Electronic commerce is the one application that used the combination of internet and information system or information technology. The combination between information technology or information systems with internet is a technology that used acquire and processed information to support the organizations (higher education) in achieving its objective. However, every organizations (higher education) who want to develop and implement the electronic commerce needs to design information system. Information systems need to be linked with organizations strategy because if it is not controlled and lined up with the organizations strategy, it will disable the organizational ability in the competitive advantage. This study aims to propose a design science research methodology which refers to the four main phases of information technology artifacts (constructs, models, methods and instantiations) to design an effective electronic commerce information system. Moreover, the implementation of design science research methodology also to be guideline to analysis the strategic information system alignment between the organizations strategy with information system planning. Through case study of Taiwan Tech in developing the security of electronic commerce system, this study conclude that design science research methodology is a very effective, efficient and easy to understand for the Taiwan Tech as a Higher Education in order to development an electronic commerce system.

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