This paper proposes a method to control structural vibrations by arranging obstacles to divert the bidirectional crowd flow. A modified social force model that takes into account pedestrian self-stopping and deceleration avoidance is used to simulate the bidirectional crowd movement. Each pedestrian is regarded as an MSD model to establish a coupled system of human-structure interaction and vibration control equations， and calculate the vibration response of the structure. A laboratory footbridge is used as an example to investigate the effect of obstacle placement on pedestrian walking characteristics and structural vibration， and to explain the damping mechanism from an energy perspective. The results show that the structural vibration caused by the bidirectional crowd density exceeding 0.6 pedestrians per square meter leads to pedestrians’ discomfort， and after arranging four obstacles on the pedestrian bridge， the vibration reduction rate reaches 12.4% and 13.1% for the two directions with one pedestrian and two pedestrians， respectively， and the energy input to the structure is significantly reduced. The reduction rates of mass kinetic energy， viscous damping energy， and elastic strain energy output of the structure reached 38.46%， 67.48%， and 50.68%， respectively. The research can provide ideas for vibration reduction methods for large-span pedestrian bridges.