The integration of STEM disciplines is increasingly advocated because it is one way to make learning more connected and relevant for students. How discipline integration can be achieved are varied, with reference to multidisciplinary, interdisciplinary, and transdisciplinary approaches adding to the debates. In integrated STEM education environment, teachers and students need to analyze and synthesize the learning content themselves through e.g. examining complex problems, using a variety of means and developing their own strategies to solve these problems. During this learning process, an explicit, well-organized and easy-to-reference learning resources will support the learning effectively. This paper focuses on how to organize learning resources for different integrated STEM pedagogical methods and learning tasks. Employing the idea of Web of Data and Linked Open Data, we describe the learning resources by semantic annotations understandable to both human and machines, and interlinking relevant resources according to the learning tasks and pedagogical methods. A user friendly resources searching, accessing, and visualization form in integrated STEM environment is also presented. By analyzing the goal and content of learning, an ontology is designed to represent the body of knowledge in STEM education, so the knowledge point in STEM education can be described by vocabularies in the ontology. These vocabularies serve as semantic tags for learning resources. We attach appropriate semantic tags to every learning resource by employing semantic annotation methods, and the learning resources will be organized and interlinked well according to their content and semantic information. Learners will take advantage of this content-based resources structure and improve the learning performance. Because we adopt standard data representation techniques, such as RDF, OWL and SPARQL etc., it will be convenient to implement and deploy the resources organization architecture in learning environment. We design a comparative experiment between semantic interlinked learning resources and non- semantic organized learning resources. Because of the support of semantic tag, it is easier to perform content-based semantic retrieval on semantic interlinked resources. From the aspects of student self-efficacy and learning achievement goals, we prove the effectiveness of interlinked learning resources organization proposed.