It is known that a reasonable three-dimensional fluctuating inlet boundary condition plays an important role in the accurate numerical simulation of wind field in the mountainous area. Taking Li Shui Bridge as the engineering background in this paper, the fluctuating wind field satisfying the characteristics of the wind field in the mountainous area was generated based on field measuring data processed by the weighted amplitude wave superposition (WAWS) method. The fluctuating velocity data was used for the inlet boundary of Large Eddy Simulation (LES) by the secondary development of the commercial software FLUENT. The comparison of the computational results from the proposed method and the method without considering fluctuating inlet boundary shows that the method developed in this paper can better reflect the actual flow field in the mountainous area. Finally, the wind field of the bridge in the mountainous area under different wind directions was simulated. It is found that the proposed method provides a reference for the refined simulation of the fluctuation wind field in mountainous area.