The invention discloses a punctuality error detection method for an intelligent substation merging unit. The punctuality error detection method for the intelligent substation merging unit includes the steps that a light IRIG-B code is output to the detected merging unit through a standard clock source, time is kept, and the minimum value of time migration between the first bit time of each frame of a 0-labeled message output by the detected merging unit and the second edge of the light IRIG-B code is obtained; inputting of the light IRIG-B code of the detected merging unit is removed, time is kept, and the maximum value of the time migration between the first bit time of each frame of a 0-labeled message output by the detected merging unit and the second edge of the light IRIG-B code is obtained; the minimum value is subtracted from the maximum value to obtain the punctuality error of the detected merging unit. The punctuality error detection method for the intelligent substation merging unit can directly measure the punctuality error of the message, the detection result can better reflect the influences of the punctuality error of the merging unit on message receiving IED equipment, and the punctuality error detection method has the advantages of being high in detection accuracy of the punctuality error, detecting the punctuality error conveniently and rapidly and being wide in application range.