The invention provides a circuit current differential protection method preventing an abnormal large number of a combination unit. Firstly, the point with the maximum amplitude is selected by comparing cycle current sampling values on the two sides of a circuit, if the point is larger than an abnormal threshold, the differential motion does not act, if the point is not larger than the abnormal threshold, and the point with the second largest amplitude is selected on the same side with the maximum point; secondly, the current sampling value at the maximum point position and the current sampling value at the second largest point position are respectively modified according to logic, and complete cycle Fourier transform is carried out to obtain current phase magnitudes at the two ends; lastly, current differential protection judgment is constructed to achieve failure judgment. According to the circuit current differential protection method, the differential protection false action caused by the abnormal large number of the combination unit of an intelligent substation can be effectively prevented by processing the large number of the sampling values, and the circuit protection reliability is improved.