Flat clinched joints are increasingly being investigated due to the flat bottom surface. In the current study, the shape of the flat clinching tools was optimized to improve the joint strength. Experimental tests of flat clinching were carried out using different forming loads to provide validation data for finite element simulations. Cross-tension tests were conducted under quasi-static conditions to evaluate the mechanical characteristics of the joint samples. Multiple finite element models based on the response surface method were developed to obtain the functional relationship between the four tool parameters and neck area, as well as the functional relationship between the four parameters and undercut area, respectively. The geometric effects of the flat clinching tools on the neck and undercut areas were analyzed. A genetic algorithm was used to obtain a solution set that maximized both the neck and undercut areas. The cross-tension strength of the joint produced according to the best-tested solution was 1526 N, which was 13.7% higher than that of the pre-optimized joint. The optimization method in this study could effectively improve the joint strength of the flat clinching process.