Data is exploding in the age of big data, and the users’ requirements for knowledge organization level are increasing day by day. Aimed to the characteristics of problem and the data to solve the problem which are multiple, redundant, complex, chaotic and new, the traditional first organizing mode could not solve the users’ problems effectively. Therefore, in this paper question driven construct the knowledge organization from the macro level, with the help of knowledge granularity and knowledge unit to design its process, and knowledge is stored on knowledge warehouse through the navigation of question to acquire, order, associate, regenerate and apply the knowledge unit. According to the different types of problems, the knowledge unit network is built oriented to the question based on node of knowledge unit and tie of knowledge relation. Mine the evolution rule from question to knowledge unit and question answered, promote the generation of the new knowledge unit. Ultimately knowledge service is provided for the application of water information efficiently and actively, with promoting the sharing, innovation and application of knowledge.