The invention provides an automatic fare collection system applicable to intercity barrier-free payment area interconnection of urban rail transit, which comprises at least two urban rail transit automatic fare collection systems, and is characterized in that the urban rail transit automatic fare collection system comprises a clearing center system, a line center computer system, a station computer system, terminal equipment, ticket cards and a backbone transmission network connecting the systems; the clearing center system of each city is interconnected with other ticket card selling businessentities in the city through the network; and the clearing center systems of the cities are interconnected through the network to share intercity ticket transaction data. The automatic fare collection system provided by the invention adjusts management modes such as system transaction clearing, keys, ticket services, clocks, blacklists and operations between the cities through interconnecting theautomatic fare collection systems of the cities, and realizes payment area barrier-free connection of the system after intercity connection of urban rail transit lines, thereby facilitating the travel of intercity citizens, saving the transfer time, improving the service level of rail transit of two cities, and avoiding a circumstance that the rail transit of two cities are connected but system services are separated.