The accuracy of the merging unit directly affects the safe and stable operation of digital substations and even smart grids. For this reason, the accuracy and real-time performance of the merging unit error check are improved from the aspects of hardware design and algorithm research. The hardware design principle of the merging unit check system is given in detail, and the spectrum phase correction based on the minimum side lobe convolution window is proposed. The algorithm realizes the accurate estimation of the unit difference and angular difference of the merging unit, establishes the merging unit clock error check scheme, and realizes the clock error check, punctual function test and absolute delay calculation. The experimental results show that the digital substation merging unit automatic error checking system designed in this paper runs stably and reliably, and meets the actual measurement requirements..