In this paper we focus on incorporating adaptive presentation and 3D visualization into Web-based learning environments to enhance learners' learning outcomes, especially to facilitate learners' spatial reasoning on geometric topics in computer graphics. This system is called CooTutor (Coordinate Tutor). According to educational media studies, "Media and Method" are the main concerns of developing such a system. In CooTutor, interactive 3D media is used to present spatial relations effectively to the learners. Instructional methods and strategies are embedded in its adaptive mechanism by incorporating ITS (Intelligent Tutoring Systems) techniques. Since geometric transformation is the example domain of our study, learners' spatial ability is considered as an index for adapting the presentation. To achieve better abstraction and flexibility, we have chosen to separate the concept sequencing from the underlying learning materials. We believe that Web-based learning could take more advantages of available computing power to enhance learning by realizing innovative instructional design, as in the case of 3D interactive presentation.