Acquiring microscope operation skills has been contained by Japanese secondary education. Although many chances of observation with the microscope operation must inspire students to study deeply science, the curriculum allows short time and small budget. In this paper, a virtual reality (VR) system of self-learning for the microscope operation is proposed, which makes inexperienced students equip fundamental skill of the operation. The system, composed by a computer, a head-mounted-display (HMD) and a dial type input device, display the student a virtual microscope in the center of the virtual world. In the virtual world, the student can manipulate the virtual microscope with controllers and a dial type input device, as well as he/she can see the procedures of the operation. The operation to focus with focus knob is especially important in the procedure, so the system adopts a dial type input device to experience under the condition more similar to the reality by the sense of touch. The system displays how to operate a microscope by visual information in texts and figures and judges if user’s operation is correct by comparing result of user’s operation and the correct one stored in the system such as the position and inclination of virtual objects. If the user operates the virtual microscope incorrectly, the system represents an alert with audiovisual stimulation. The system is expected to help users to learn microscope operation skills practically at relatively low cost.