With the acceleration of the urban development process and the rapid growth of China's population, the subway has become the first choice for people to travel, and the urban underground space has been continuously improved. The subway construction has become the focus of urban underground space development in the 21st century. During the construction of subway tunnels, the problem of surface settlement will inevitably be caused, and the problem of surface settlement will have a certain safety impact on the safe use of surface buildings. The impact of surface construction is predicted, so as to select the best construction technology and avoid the problem of surface subsidence to the greatest extent. On the basis of analyzing the principle of surface subsidence, this paper studies the optimal control strategy and process of subsidence in subway tunnel engineering. The research results of the article show the following. (1) The two sections of the pebble soil layer have basically the same subsidence trend. Among them, the first section has a larger settlement amplitude and both sides are steeper. The second section is mainly cobble clay soil. The pebble layer has good mechanical properties. If it can be well filled, its stability will be improved. The comparative analysis of the two sections shows that with the increase of the soil cover thickness, the maximum subsidence at the surface gradually decreases. The reason is that when the stratum loss is the same, the greater the soil cover thickness, the greater the settlement width. Sections 2 and 3 of a single silty clay have relatively close settlement laws, and the settlement changes on both sides of the tunnel are similar. (2) The surface subsidence caused by the excavation of the side hole accounts for more than 50% of the total surface subsidence, and the width of the settlement tank after the excavation of the side hole is increased by 8–10 meters compared with the excavation of the middle hole. (3) The prediction error of the BP neural network model proposed in this paper is the lowest among the four models, whether it is the prediction of the cumulative maximum surface subsidence or the location of the cumulative maximum surface subsidence, and the average relative error of the cumulative maximum surface subsidence is 3.27%, the root mean square error is 3.87, the average relative error of the location of the cumulative maximum surface subsidence is 7.96%, and the root mean square error is 21.06. In the prediction process of the cumulative maximum surface subsidence, the prediction error value of the Elman neural network is relatively large, and the GRNN generalized neural network and RBF neural network have no significant changes; in the process of predicting the position where the cumulative maximum surface subsidence occurs, the prediction error value of RBF neural network is maximum.