The invention relates to a vehicle wading warning and protecting system and a control method thereof. The system comprises an engine ECU (Electronic Control Unit), a vehicle ignition control module, a vehicle oil injection control module, at least two groups of water level sensors, a micro ECU, a micro power supply, an air inlet passage choke valve device and at least two water level warning lamps, wherein the vehicle ignition control module and the vehicle oil injection control module are connected with the engine ECU; the water level sensors are arranged on a vehicle body from bottom to top according to warning levels from low to high; the position of each water level sensor at the highest warning level is lower than that of an air inlet of an air filter of a vehicle; the signal output ends of the water level sensors at the highest warning level are connected with the engine ECU; the signal acquisition end of the micro ECU is connected with the signal output ends of the at least two groups of water level sensors; the instruction output end of the micro ECU is connected with the air inlet passage choke valve device and the water level warning lamps; the micro power supply is connected with the power supply end of the micro ECU; the air inlet passage choke valve device is arranged on an air inlet passage of the vehicle and is used for controlling opening and closing of the air inlet passage; the number of the water level warning lamps is the same with the group number of the water level sensors. According to the vehicle wading warning and protecting system and the control method, a water depth can be effectively prompted to a driver, and an engine and electrical appliances of the whole vehicle are effectively protected from being damaged.