The rapid development of network technologies has made the web a huge information source with its own characteristics. In most cases, traditional database-based technologies are no longer suitable for web information processing and management. For effectively processing and managing web information, it is necessary to reveal intrinsic relationships/structures among concerned web information objects such as web pages. In this work, a set of web pages that have their intrinsic relationships is called a web page community. This paper proposes a matrix-based model to describe relationships among concerned web pages. Based on this model, intrinsic relationships among pages could be revealed, and in turn a web page community could be constructed. The issues that are related to the application of the model are deeply investigated and studied. The concepts of community and intrinsic relationships, as well as the proposed matrix-based model, are then extended to other application areas such as biological data processing. Some application cases of the model in a broad range of areas are presented, demonstrating the potentials of this matrix-based model.