The invention discloses an underwater three-dimensional scanner and a control method thereof. The underwater three-dimensional scanner comprises an upper computer, a sealed cabin, a line laser, an illumination module, an imaging module, an attitude sensor and a communication module, wherein the line laser, the illumination module, the imaging module, the attitude sensor, and the communication module installed in the sealed cabin. The line laser, the illumination module, the imaging module, and the attitude sensor are connected with the upper computer through the communication module. The underwater three-dimensional scanner is reasonable in structure and simple in operation, and three-dimensional reconstruction information of the underwater target object can be obtained rapidly.