With the rapid urbanization and expansion of rail transit systems, the axle loads of trains, which are a critical aspect of their configuration, have significantly increased. This increase poses substantial potential threats to the safety and service life of existing bridges within urban rail transit networks. Therefore, it is imperative to develop methods for monitoring and identifying train axle loads. In this study, a strain field measurement scheme was devised and implemented for an operational simply supported composite beam bridge in urban rail transit. This involved numerical modeling and validation of the bridge’s structural response, followed by the calculation of strain influence lines at specific measurement points. Subsequently, a method for identifying train axle loads, considering the dynamic amplification effect, was established. This method integrates principles from strain influence lines with mathematical optimization techniques. Specifically, the axle loads of locomotives on the forward AC03 type trains of Shanghai Metro Line 3 were found to conform to a logarithmic normal distribution model, while those of middle carriages followed a normal distribution model. Their respective mean axle loads were determined as 9.64 t and 10.77 t, with a shared variance of 0.8. Similarly, the axle loads of locomotives and middle carriages on reverse AC03-type trains also followed normal distribution models, with identical mean values around 10.5 t. The variances for axle loads of locomotives and middle carriages of reverse trains were found to be 1.36 and 0.8, respectively. The developed method effectively enables the monitoring of train axle loads and assessment of their impact on bridge structures, therefore enhancing safety and operational reliability within urban rail transit systems.