The invention discloses an engine cylinder center distance measurement system and a measurement method thereof. The measurement system comprises a measurement body; two sides of the measurement body are symmetrically provided with measurement units; one side, deviating from the measurement units, on the measurement body is provided with a measurement gauge capable of displaying the measurement result of the measurement unit; the measurement units are electrically connected with the measurement gauge; each measurement unit comprises a measurement rod with the same radius as the inner part of the engine cylinder; one end part, close to the middle part of the measurement body, of the measurement rod is fixedly provided with a guide rail; a spring sleeves the guide rail; a sliding block is arranged between the spring and the measurement rod; the spring is fixedly connected with the sliding block; and the other end of the spring is fixedly arranged on the guide rail. The measurement methodis based on the above measurement system. The system and the method are applicable to engine cylinder center distance measurement during a production line batch processing process, the production input cost is reduced, and the structure is simple and convenient.