A method for mass spectrometry data analysis for estimating a structure of an unknown substance produced through partial structural change from a known substance having a known structure based on MS n spectra where n is an integer equal to or greater than 1 obtained by performing mass spectrometry of product ions produced by dissociating, in one or a plurality of times, a precursor ion or ions originating from the unknown substance, the partial structural change comprising the elimination of an unknown eliminating partial structure and the addition of an additional partial structure, the method comprising: a) an additional partial structure information obtaining step of obtaining pre-given information of an additional partial structure; characterized by b) a post-elimination structure estimating step of estimating a post-elimination structural formula (A') after an unknown eliminating partial structure is eliminated from the known substance as a candidate for the post-elimination structural formula (A'), the estimation being performed based on pre-given information about structural formula of the known substance, information about an additional partial structure obtained in the additional partial structure information obtaining step, and information about a mass of the precursor ion from the unknown substance obtained from an MS n spectrum or MS n spectra of the unknown substance; c) a product ion structure estimating step of estimating a structural formula of each of product ions by searching for coincidence of a combined mass of a trunk partial structure and the additional partial structure and masses of product ions obtained from the MS n spectrum or MS n spectra of the unknown substance, the trunk partial structure being derived from a structure shown by a structural formula of the candidate for the post-elimination structural formula (A'), and listing candidates for structural formulas of the product ions; and d) an unknown substance structure determining step of determining a structural formula of the unknown substance by searching, based on the candidates for structural formulas of the product ions estimated in the product ion structure estimating step, for a structural formula that can produce the candidates for the structural formulas of product ions by dissociation. a) an additional partial structure information obtaining step of obtaining pre-given information of an additional partial structure; characterized by b) a post-elimination structure estimating step of estimating a post-elimination structural formula (A') after an unknown eliminating partial structure is eliminated from the known substance as a candidate for the post-elimination structural formula (A'), the estimation being performed based on pre-given information about structural formula of the known substance, information about an additional partial structure obtained in the additional partial structure information obtaining step, and information about a mass of the precursor ion from the unknown substance obtained from an MS n spectrum or MS n spectra of the unknown substance; c) a product ion structure estimating step of estimating a structural formula of each of product ions by searching for coincidence of a combined mass of a trunk partial structure and the additional partial structure and masses of product ions obtained from the MS n spectrum or MS n spectra of the unknown substance, the trunk partial structure being derived from a structure shown by a structural formula of the candidate for the post-elimination structural formula (A'), and listing candidates for structural formulas of the product ions; and d) an unknown substance structure determining step of determining a structural formula of the unknown substance by searching, based on the candidates for structural formulas of the product ions estimated in the product ion structure estimating step, for a structural formula that can produce the candidates for the structural formulas of product ions by dissociation.