A spectral image data processing apparatus which conducts multivariate analysis on spectral image data of a sample, including: a region setting unit configured to set a region of interest for performing multivariate analysis in a sample in which a difference needs to be distinguished, the region of interest being set in accordance with spectral image data of the sample; and an analysis unit configured to perform the multivariate analysis with spectral image data inside the region of interest and spectral image data of region of non-interest which is a region other than the region of interest being distinguished from each other.