The invention relates to a sampling data exception detecting method and a relay protection method based on redundant CT windings, and belongs to the technical field of relay protection of electric power systems. Sampling data of two CT windings of a mutual inductor are used for mutual inspection, namely deviations of two paths of A/D (analog/digital) sampling data of the two windings are respectively compared, the sampling data at a certain sampling point are judged abnormal when both absolute deviation and relative deviation of the momentary value of the sampling point are larger than a set threshold, the sampling point is repaired by an interpolation algorithm when only the sampling point is abnormal, the A/D sampling data are judged abnormal when a plurality of continuous sampling points are abnormal, the sampling data are automatically switched to the second path of A/D sampling data when the first path of A/D sampling data is abnormal, latch-up protection is performed if the second path of A/D sampling data is also abnormal, accordingly, normal running of a protector is unaffected when only one path of A/D sampling data is abnormal, and reliability of the protector is improved.