In the field of economic research, most of the sample data is not obtained based on controllable experiments but generated during the normal operation of the economic system. Therefore, the change of an economic variable is usually not caused by a single change of a cause variable. It is the result of a combination of multiple factors. Therefore, it is necessary to study the application of mathematical intelligent computing in computer intelligent manufacturing system. The purpose of this paper is to explore the application of mathematical intelligent computing in computer intelligent manufacturing system. For this reason, this paper uses the furnace temperature control model to carry out simulation experiment. In this simulation experiment, three algorithms of mathematical intelligent computing are mainly used, including BPES intelligent computing method, genetic algorithm, and MARS algorithm. The research results show that the superparameter optimization based on MARS has high efficiency, and the best result, the worst result, the average result, the variance, and the average time of multiple independent runs are controlled below 0.03 s. In this experiment, when the hidden layer node is 9, the prediction error value is the smallest, and the model simulation curve is basically consistent with the measured curve trend. In the simulation experiment of this paper, these three algorithms have shown good results in their respective links.