In this article, a mathematical analysis model of economics of prefabricated building structure based on improved neural network algorithm is proposed in order to solve the low analysis accuracy in traditional methods. Firstly, by means of analyzing the costs of materials, labor, and equipment, the economic characteristics of the cost of fabricated building structures are determined. Secondly, the single neuron is analyzed and the weight coefficient is adjusted in accordance with the multilayer neural network structure, so as to minimize the construction error of the economic analysis model of the assembled building structure. Meanwhile, the weight vector is obtained, error-weighted square sum is calculated through choosing an adaptive filter and obtained, and the weight vector is updated by the least squares algorithm. Thirdly, the neural network algorithm training and learning process is designed and improved, the dependent variable is selected, the number of input points is determined, and then, the training and learning process of the improved neural network algorithm is completed. Finally, a fitness function is set to measure the authenticity of dataset, which is further defined as a combination of different weights to construct an economic mathematical analysis model. The experimental results indicate that the analysis results of this method can reach an accuracy up to 96%, so it has a broader application prospect in low-rise buildings.