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This paper reveals weaknesses of existing e-learning system and puts forward a novel architecture of five layers from the perspective of knowledge innovation. Learner interface layer is a portal that learners enter the system and exploit the offered functionality. Layer of collaborative learning environment is the space where learners collaborate to learn and create new knowledge by doing projects. Knowledge processing layer processes knowledge produced and identifies whether is new. Knowledge access layer based on PHP is used to accessing knowledge and resource bases. The last layer is knowledge and resource bases which are supported by My SQL server.