By nature, an E-Learning system includes two aspects–learning and technologies. In the perspective of learning, learning contents (knowledge) and learning resources are the main parts of an E-Learning system; technologies are only means or tools which will be used to support learning process. With the popularization and deeper application of E-Learning systems, more and more network courses and learning resources have been developed. Accordingly, many problems have being occurred too, such as the difficulty of curriculum developing and updating, the flexibility, expansibility and maintainability of an E-Learning system, etc. On the basis of research about learning contents and their management, i.e., knowledge body of a discipline, we proposed a discipline oriented common knowledge ontology base based layering architecture of E-Learning system. In this developing mode, a common knowledge ontology base (KOB) in a discipline will be built, then through it, the problems of curriculum developing, course contents updating, learning contents reusing among different courses and the learning resources management will be solved, so to ensure the flexibility and practicability of E-Learning systems.