A system for remotely controlling microscopic machinery and a method thereof are provided. The system includes at least one local device and a remote host for sending a control command thereto. A microslide is placed on a microscopic camera device in the local device, and the microscopic camera device captures an image of the microslide according to a capture command in the control command. The local device transmits the image to the remote host in a video format. A motorized stage moves to a next preset position according to a movement command in the control command to capture another image of the microslide. The steps of capturing and transmitting the image and the step of moving are repeated until the microslide is captured completely. The invention can solve the problem of time delay when the image captured by the remote control microscopic camera device is displayed.