With the full speed development of the hydropower project of our country, hydropower station is playing a greater and greater role to adjust peak, modulate frequency, adjust phase in large-scale electric network and guarantee the electric network safe running, so it has very important meanings to accurately discover and locate the trouble of hydropower unit for the stable and reliable running of power system and healthily and continuously development of national economy. At present, there are a lot of research results about the trouble diagnosing method and system of hydropower unit, but these research results have not reached the anticipated result in the concrete trouble diagnosis because did not merge the diagnosis method and system organically. This paper set up a trouble diagnosis system of hydropower unit based on Multi-Agent, this system is composed of five Multi-Agent subsystems such as management, state monitoring, signal pretreatment, symptom extracting, trouble diagnosing, etc., each subsystem is formed by a lot of Agent also. This system can fully utilize good intelligent of Agent and good communication harmony within Multi-Agent system, so can greatly improve the realtime character of trouble diagnosis of hydropower unit.