A multiple electronic control unit (ECU) diagnosing system and a method thereof for a vehicle by which a diagnosis time for an ECU can be shortened by using an Ethernet protocol and a communication gateway. The multiple ECU diagnosing system for the vehicle applies a multiple ECU diagnosing algorithm of a one-to-n method which is more efficient than a diagnosis algorithm of a one-to-one method between diagnostic equipment. ECUs for the vehicle are connected through various communication networks (K-Line, CAN, LIN, FlexRay, and MOST) by using a communication gateway transferring messages and signals between the ECUs, thus significantly shortening a diagnosis time for the ECUs and acquiring a large amount of diagnosis information at the same time.