The urgent train braking could bring structural response menace to the bridge under passive control. Based on the analysis of breaking dynamics of a train-bridge vibration system, a magnetorheological elastomeric bearing (MRB) whose mechanical parameters are adjustable is designed, tested and modeled. A finite element method (FEM) is carried out to model and optimize a full scale vibration isolation system for railway bridge based on MRB. According to the model above, we also consider the effect of different braking stop positions on the vibration isolation system and classify the bridge longitudinal vibration characteristics into several cases. Because the train-bridge vibration isolation system has multiple vibration states and strongly coupling with nonlinear characteristics, a human-simulated intelligent control (HSIC) algorithm for isolating the bridge vibration under the impact of train braking is proposed, in which the peak shear force of pier top, the displacement of beam and the acceleration of beam are chosen as control goals. The simulation of longitudinal vibration control system under the condition of train braking is achieved by MATLAB. The results indicate that different braking stop positions significantly affect the vibration isolation system and the structural response is the most drastic when the train stops at the third cross-span. With the proposed HSIC smart isolation system, the displacement of bridge beam and peak shear force of pier top is reduced by 53.8% and 34.4%, respectively. Moreover, the acceleration of bridge beam is effectively controlled within limited range.