The disclosure discloses an inhomogeneous sample equalization method and system for a product assembly process. The method includes the following steps of: A: calculating a similarity among different samples; B: constructing a fuzzy compatibility matrix S for representing the similarity among all the samples, and constructing a fuzzy compatibility space X with different granule layers through the fuzzy compatibility matrix S; C: based on a granular calculating mode, screening out a granule layer with a maximum comprehensive value of an information increment and the similarity among the samples from the fuzzy compatible space X to serve as an optimal granule layer; and D: carrying out equalization processing on the sample of the optimal granule layer.