In complex industrial processes, it is necessary to perform modeling analysis on some industrial systems and find and optimize the factors that have the greatest impact on the results, in order to achieve the optimization of the industrial systems. However, due to the high-level nature or complex working mechanism of complex industrial systems, traditional principal component analysis methods are difficult to apply. Therefore, this paper proposes a characteristic model-based principal component analysis (CMPCA) to perform principal component analysis on complex industrial systems. The differential pressure flowmeter is taken as an example to verify the effectiveness of the method. Flowmeter is an indispensable instrument in measurement, and its accuracy depends on its own structural parameters. However, the measurement accuracy of some flow meters is not high, and the measurement error is large, which affects the normal industrial production process. This method is used to analyze the influence of the structural parameters of the flowmeter on its measurement accuracy, and the four most important structural parameters are found and optimized. The measurement error of the Bitoba flowmeter is reduced from 1% to 0.2%, and the measurement repeatability is reduced from 0.3 to 0.06, which proves the effectiveness of the method.