Information outsourcing had great accomplishments such as application of professional technologies in private sector and improvement of service quality, while it was thought to have resulted in many internal management problems. This research use transaction cost theory to compare and analyze transaction cost and cause of transaction cost in information system outsourcing. Operation and maintenance of e-trade service and customs office were chosen as subject of this research, and transaction cost was analyzed. For e-trade service, complexity of work and complexity of system were main cause of transaction cost, when they established business plans, reviewed program proposals, and adjusted changes. For maintenance and operation in Customs Office, major cause of transaction cost were environmental uncertainty, legal factors, and security when they confirmed the business, wrote an RFP, reviewed RFP, and estimated expected cost. This research has theoretical significance because it analyzed relationship between transaction attribute and transaction cost, and also political significance because it proposed the way to lower transaction cost in information system outsourcing.