Along with fast progress in their ability and flexibility, more robots are introduced for automation, and applied for more complicated tasks. Consequently, it demands more versatile and advanced manipulative devices for task manipulation and teaching. We thus propose a novel manipulation system based on virtual reality (VR). This system is intended for achieving 3D manipulation in a real-time manner. VR is recognized for capable of providing immersive feeling for the user. Meanwhile, it also faces the challenge in making the VR environment as close as the real one. To tackle this, we propose building a point cloud model of the real environment and integrating it with the virtual one. Meanwhile, to ease the load of the user during manipulation, we also develop a user-friendly interface, including a mechanism that can adjust the resolution of the command according to task complexity. Experiments are conducted to evaluate system's performance, and questionnaires administered for acquiring user's feedback.