In this study, one innovative Virtual Manipulatives and Whiteboard system, called VMW, was proposed. The VMW system facilitated users to manipulate virtual objects in 3D space and figure out to find clues in solving geometric problems. Meanwhile, users can generate appropriate translucent multimedia whiteboards in any viewpoint of 3D space to express their mathematic solution and verbal explanations tightly combined with the 3D theme manipulated behind. Thus, users can easily use multiple representations like manipulation or symbolic terms to organize their thinking in geometry problem solving based on the pedagogical theory, “Children would construct their geometry concepts from multiple representations like mapping the concrete items to abstract ideas through physical or mental manipulation“. The proposed system was evaluated with one pilot study to investigate its perceived ease of use and usefulness. Furthermore, students’ solving strategies were analyzed from their manipulation in the 3D space and solutions in the whiteboards. The results showed our proposed system was perceived useful and had positive effects for solving geometry problem.