The invention relates a method for identifying the failure of the sampling value data of an intelligent substation based on a waveform coefficient equation. The method comprises the following steps that: a relay protection device establishes data models of different protection units according to the difference among the protection units, wherein the data models comprise a differential protection data model, an impedance protection data model and a direction protection model; the data output by the unconventional mutual inductor of the intelligent substation is directly switched in the relay protection device in a digital mode through a combination unit and via a switch or without via a switch, the relay protection device performs mathematical operation according to the sampling value data of voltage and current input into the unconventional mutual inductor, and the waveform coefficient of a sampling value is calculated according to the data models of the different protection units; and the relay protection device judges the size and fluctuation range of a formed waveform coefficient value to judge whether relay protection is shut.