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The design scheme of a small and portable flow meter calibration system was proposed in this paper. And an improved collaborative optimization algorithm was applied to calculate the optimum solution of the design variables in each subject. Firstly, the algorithm idea and the improvement method were introduced. And the design variables, objective functions and constraint conditions of each subject were established according to the design requirements. Secondly, the genetic algorithm was used to calculate the optimal solution of each design variable, and the design scheme was improved based on the optimization results. In addition, the feasibility of the optimization results was verified by computer simulation and other methods. The results showed that the optimized calibration system met the design requirements of hydrodynamic effect, uniform motion time and system weight, and the effectiveness of collaborative optimization algorithm in solving multidisciplinary design optimization problems was proved.