The invention relates to the highway toll payment field, and especially relates to a highway toll mobile payment system and method based on a mobile end application and license plate identification. The system comprises a mobile payment APP, entrance/exit lane subsystems, a mobile payment operation management platform, a mobile payment gateway, a money collection and electronic invoice subsystem,and a province network clearing and settling center. The entrance/exit lane subsystems include license plate identification devices installed on all entrance/exit lanes, lane barrier gate controllers,and entrance/exit computers. The license plate identification devices at entrances/exits are adopted to collect license plate numbers of vehicles that pass by, the license plate numbers are input toa mobile payment background system, running paths of the vehicles are recorded through the license plate numbers, bound APP accounts are queried through the license plate numbers, and tolls are paid through a mobile terminal such as a mobile phone. In this way, mobile payment of tolls is realized, the lingering time of the vehicles at highway entrances/exits is reduced, and the pass speed is increased.