The invention discloses an analysis method for predicting body weight increase caused by treating schizophrenia through a second-generation antipsychotic based on the polygene combination interactiveeffect. The method comprises the steps that a sample is prepared for collecting peripheral blood of a patient with body weight increase caused by treating schizophrenia through the second-generation antipsychotic, a hypotonic salt fractionation method is used for extracting a genome DNA sample; a MODLI-TOF flight mass spectrum detecting method is used for performing genetic typing of a 5-HT2CR gene, a histamine 1 receptor gene, an oxytocin gene, an NPY / R gene, a Leptin gene, an adiponectin gene, an FGF21 gene and a FGF23 gene; data analysis and extraction are performed, instrument original data is aligned, data with no noise interference for statistic analysis is obtained, a generalized multi-factor dimension reduction method is used for performing the quantitative trait gene-gene interaction effect, crossed verification is further applied, and the gene interaction effect is used for predicting body weight increase. By adopting the generalized multi-factor dimension reduction method, the continuous ending variable is processed, covariance is introduced, and the method has the advantages of greatly enlarging the application range and greatly increasing the prediction accuracy.