In recent years, the global pandemic promotes the development of online teaching. Research on the technology that enables high-quality online teaching is of great importance to the global pandemic. But whether the digital teaching resources can be used reasonably and effectively in the teaching process has direct influence on teaching quality and outcome. The traditional textbooks build a linear, tree-type structure in the form of “chapters, sections, and pages”. However, what the knowledge system should present essentially is a net-type structure. Besides, the tree-type structure could not show the transverse association between knowledge points. In this paper, we propose a new knowledge organization technology of 3D topic map. Based on this map, we organize the construction of knowledge, and the common types of online teaching resources for visual presentation. Firstly, we expound the formal description, relational reasoning, and the construction of knowledge navigation path based on 3D topic map; Secondly, we analyze the form of knowledge representation combining multimedia technology and virtual simulation technology; Finally, taking the application of 3D topic map in part knowledge domain of “Computer Fundamentals” course as an example, we discuss the organization, management, and service of 3D topic map for common types of online teaching resources. The proposed 3D topic map provides a new technical reference for organizing and managing online teaching resources and promoting the effect of online teaching.