High-speed railway suspension bridges (HSRSBs) have been constructed with the new advancements in technology. The deformation prediction for HSRSBs is essential to their safety and maintenance. The conventional prediction methods are developed for bridges without high-speed railway. Different factors, including temperature (TEMP), time delay compensation (TDC), train live load (TLL), are considered in these methods. However, the train side (TS) and train instantaneous position (TIP) have a significant impact on deformation for HSRSBs, and they are not used in the prediction. More importantly, the coupling issue among different factors is so significant that it cannot be neglected. In this study, we propose a deformation prediction model based on a backpropagation (BP) neural network. This model uses different factors as model input, including TEMP, TDC, TLL, TS, and TIP. The coupling issue is addressed by using the new model. The new model was evaluated using a dataset of 10-day field measurements. It achieves a mean absolute error (MAE) of 8.81 mm, a mean relative error (MRE) of 9.82%, and coefficient of determination (R2) of 0.94. The new model will provide high-precision prediction for deformation and will be used in the development of an early warning system.