In this study, a modeling tool named UP Finder was developed based on the COBRA toolbox. It facilitated the rapid identification of gene overexpression strategies to assist pathway design in metabolic engineering of targeted overproduction. Gene targets with highly related to overproduction were determined by a quantitative evaluation procedure. The graphical user interface of the UP Finder provided easier access for analyzing various targeted products in different microorganisms. Analysis examples for overproducing lycopene precursor and fatty acyl-ACP by the UP Finder showed high degree of agreement with the reported key genes in the literatures.