In the process of aircraft assembly, workpieces are located and supported by flexible locators on assembly fixture, which is reconfigurable and flexible. However, the assembly accuracy is decreased for the existence of flexible locating errors caused by flexible deformation when vertical assembly is involved in assembly fixture. To increase the assembly accuracy of vertical assembly in reconfigurable flexible fixture, the research on the strategy of flexible error control is developed. Firstly, the locating error is analyzed and traced according to the features of structure and theories of locating/supporting. Secondly, the influence of flexible locating errors is reduced by optimizing the locating/supporting layout. Considering the constraints caused by features of workpieces, the mathematical model of constraints is built based on the feasible design region, therefore, the repairing method is presented as well as the corresponding optimization algorithm is improved. Finally, the optimization is conducted by calling parameterized model based on APDL language in MATLAB environment. As a result, the availability of the improved algorithm and the feasibility of the error control strategy are demonstrated by simulation result that the assembly accuracy is promoted by the optimized locating/supporting layout.