In the present investigation, a wind tunnel experiment was performed to evaluate the effectiveness of the trailing edge jets control scheme to mitigate the unsteady aerodynamic force and flow structure of a single box girder (SBG) model. The flow control scheme uses four isolated circular holes for forming the jet flow to modify the periodic vortex shedding behind the SBG model and then alleviate the fluctuation of the aerodynamic force acting on the test model. The Reynolds number is calculated as 2.08 × 104 based on the incoming velocity and the height of the test model. A digital pressure measurement system was utilized to obtain and record the surface pressure that was distributed around the SBG model. The surface pressure results show that the fluctuating amplitude of the aerodynamic forces was attenuated in the controlled case at a specific range of the non-dimensional jet momentum coefficient. The Strouhal number of the controlled case also deviates from that of the original SBG model. Except for the pressure measurement experiment, a high-resolution digital particle image velocimetry system was applied to investigate the detailed flow structure behind the SBG model to uncover the unsteady vortex motion process from the SBG model with and without the trailing edge jets flow control. As the jet flow blows into the wake, the alternating vortex shedding mode is switched into a symmetrical shedding mode and the width of the wake flow is narrowed. The proper orthogonal decomposition was used to identify the energy of the different modes and obtain its corresponding flow structures. Moreover, the linear stability analysis of the flow field behind the SBG model shows that the scheme of trailing edge jets can dramatically suppress the area of unsteady flow.