The combination of large tooling size, environmental vibration, and equipment errors at the aircraft assembly site leads to errors in the enhanced reference system (ERS) point measurement information. ERS point errors directly reduce the accuracy of the assembly measurement field. This paper proposes ERS point error prediction and registration compensation based on the neural network to address this problem. First, the effects of equipment measurement errors and environmental vibration factors on the measurement field are studied. The ERS point error prediction model based on the neural network is established. On this basis, model evaluation is used to assess the prediction model of this paper. Then, a measurement field registration compensation model is constructed based on the neural network error results for ERS point compensation analysis. Finally, an experimental validation platform was built to predict the ERS point errors and compensate for the constructed measurement fields using the method in this paper. The experimental results show that, compared with the conventional method, the maximum registration errors in the X, Y, and Z directions are reduced from 0.0812, −0.0565, and −0.2810 to −0.0184, −0.0010, and 0.0022 mm, respectively, after compensation in this paper. The method proposed in this paper can not only predict the ERS point error state and provide a reference for designers but also guide the selection of appropriate ERS points when constructing the measurement field. The compensation method in this paper effectively reduces the measurement field registration error.