There are provided an electrophoresis measurement method which can easily and accurately judge degree of similarity between reference data and measurement target data, a data processing device, and a data processing program. Detected data obtained by subjecting a reference sample to electrophoresis is standardized with reference to peaks of a lower limit marker substance and an upper limit marker substance, and thus reference data is acquired. Detected data obtained by subjecting a measurement target sample to electrophoresis is standardized with reference to peaks of the lower limit marker substance and the upper limit marker substance, and thus measurement target data is acquired. The measurement target data is warped or shifted in a time axis direction with reference to the reference data, and corrected measurement target data is obtained.