In order to solve the problems of many boards and plug-ins, high failure rate, large size of devices faced by relay protection technology in intelligent substations, a chip-based protection design is proposed, and the architecture design of line differential protection and each functional module are developed based on ZYNQ platform. In the sampling value synchronization module, the Lagrangian quadratic interpolation method is chosen to resample and interpolate the sampling messages, and the effect of primary frequency change is eliminated by time scale correction; in the design of the Fourier transform module, the hardware advantage of field programmable gate array (FPGA) is fully utilized to ensure the speed and real-time calculation, and the function of the line differential protection is verified by simulation and dynamic mode test. The chip-based line protection device designed based on this scheme has been put into trial operation in a 500 kV substation, and it is in good operation.