In this paper, bridge alignment control with considering dynamic train loads was experimentally and theoretically investigated. Analytical process of bridge dynamics and the self-adaptive Kalman filter bridge alignment control method with considering the dynamic train loads were briefly introduced. The static measurement, the dynamic test, the field alignment measurement as well as the finite element analysis (FEA) of the second longest rail transit cable-stayed bridge in the world were carried out. Based on the results, the train dynamic load effect on the bridge alignment was obtained quantitatively. Subsequently, alignment control of the rail transit bridge with considering this effect using a self-adaptive Kalman filter method was analyzed. The results show that: (a) the dynamic train loads have effects on alignment control of the bridge and therefore cannot be neglected; (b) the self-adaptive Kalman filter method is applicable and reliable for alignment control of bridges during construction. The analytical method and whole process contribute to develop a related specification and further engineering applications.