The invention discloses a rail traffic axle counting system based on FPGA phase detection. The rail traffic axle counting system comprises a first wheel sensor arranged on one side of a rail and a second wheel sensor arranged on the other side of the rail, the first wheel sensor and the second wheel sensor are connected with a control room through axle counting equipment, and the axle counting equipment comprises a first FPGA, a first conditioning circuit, a second FPGA and a second conditioning circuit. The first FPGA generates a pulse signal with the frequency f1 and sends the pulse signal to the first wheel sensor through the first conditioning circuit, and a signal returned by the first wheel sensor is connected to the first FPGA through the first conditioning circuit to be subjected to data processing. The second FPGA generates a pulse signal with the frequency f2 and sends the pulse signal to the second wheel sensor through the second conditioning circuit, and a signal returned by the second wheel sensor is connected to the second FPGA through the second conditioning circuit to be subjected to data processing. The first FPGA and the second FPGA sends the counting results to the control room. The debugging efficiency is improved, and the rail traffic axle counting system is suitable for a train travelling at a high speed.