The invention discloses an intelligent flood prevention baffle system and a working method thereof, and relates to intelligent flood prevention systems. The intelligent flood prevention baffle system is good in sealing and capable of rapidly conducting intelligent flood prevention in time, and comprises a baffle system body, a sensing testing system, a remote information processing and information transmitting system, an information issuing system, a real-time monitoring system and an operation command system. The intelligent flood prevention baffle system has the beneficial effects that the overall size is small; during the flood period, baffles can be automatically and rapidly unfolded accurately, and therefore a protected object can be free of water entering; the sealing performance between the baffles and the wall is good; during the non-flood period, the baffles can be folded without influencing other kinds of work; the intelligent flood prevention baffle system can achieve automatic water draining, automatic alarming and real-time monitoring, emergency responses can be rapider accordingly, information transmission can be more accurate and rapider, and the flood defending capacity is improved; and a wireless transmission system and a wired transmission system are adopted, the stability of the transmission system is improved, and the emergency defending capacity is improved.