A monitoring system and a control method thereof are provided. The monitoring system includes a drone and a base station. The drone includes an IR detector. The base station includes a platform, a moving vehicle, an IR positioner, and a positioning apparatus. The drone is placed on the platform disposed on the moving vehicle. The IR positioner emits an infrared ray. The positioning apparatus includes a movement member and a positioning controller. The movement member is movably disposed on the platform. The positioning controller is coupled to the movement member. The drone moves to the platform according to the infrared ray. When the drone is located on the platform, the positioning controller controls the movement member to push the drone and move the drone to a specific position. Accordingly, the drone can take off or be landed immediately when the base station is moving or remains still.