An analytical data processing method that handles a spectrum data set including mass spectrum data collected by performing mass analyses respectively on a plurality of measuring points in a predetermined region to be measured set on a sample and indicating a relationship between a mass charge ratio and an ion intensity value, being associated with spatial position information of the measuring points, the method comprising: for a plurality of the spectrum data sets including the mass spectrum data whose mass resolution and/or spatial resolution is different from each other, a) an individual reference value acquiring step for obtaining, for each of the spectrum data sets, a maximum reference value at which intensity values after normalization do not exceed a predetermined allowable value when normalizing the intensity values for all or part of mass charge ratio values in the mass spectrum data at respective measuring points, the predetermined allowable value being a maximum possible value that a variable storing the intensity values can take when executing a normalization operation in the normalization executing step, and the maximum reference value being smaller than a product of the predetermined allowable value with a quotient of a respective sum of the intensity values for all or part of mass charge ratio values in the mass spectrum data at a measuring point in the predetermined region to be measured and a respective maximum intensity value for all or part of mass charge ratio values in the mass spectrum data at the measuring point; b) a common reference value selecting step for selecting as a common reference value a minimum reference value from a plurality of the reference values obtained for all the spectrum data sets in the individual reference value acquiring step or setting as the common reference value a value smaller than the minimum reference value; and c) a normalization executing step for normalizing the intensity values for all or part of the mass charge ratio values in the mass spectrum data contained in each of the spectrum data sets based on the common reference value selected or set in the common reference value selecting step, wherein intensity values for all or part of mass charge ratio values in the mass spectrum data at the respective measuring points are multiplied by a normalization coefficient which is obtained by dividing the common reference value by the respective sum of the intensity values for all or part of mass charge ratio values in the mass spectrum data at the respective measuring points. a) an individual reference value acquiring step for obtaining, for each of the spectrum data sets, a maximum reference value at which intensity values after normalization do not exceed a predetermined allowable value when normalizing the intensity values for all or part of mass charge ratio values in the mass spectrum data at respective measuring points, the predetermined allowable value being a maximum possible value that a variable storing the intensity values can take when executing a normalization operation in the normalization executing step, and the maximum reference value being smaller than a product of the predetermined allowable value with a quotient of a respective sum of the intensity values for all or part of mass charge ratio values in the mass spectrum data at a measuring point in the predetermined region to be measured and a respective maximum intensity value for all or part of mass charge ratio values in the mass spectrum data at the measuring point; b) a common reference value selecting step for selecting as a common reference value a minimum reference value from a plurality of the reference values obtained for all the spectrum data sets in the individual reference value acquiring step or setting as the common reference value a value smaller than the minimum reference value; and c) a normalization executing step for normalizing the intensity values for all or part of the mass charge ratio values in the mass spectrum data contained in each of the spectrum data sets based on the common reference value selected or set in the common reference value selecting step, wherein intensity values for all or part of mass charge ratio values in the mass spectrum data at the respective measuring points are multiplied by a normalization coefficient which is obtained by dividing the common reference value by the respective sum of the intensity values for all or part of mass charge ratio values in the mass spectrum data at the respective measuring points.