In this study, a femtosecond laser cloud and fog transmission model, which considers the nonlinear optical effect, turbulence disturbance, and particle scattering, is established based on the concept of the stratified scattering medium transmission model. Further, the influence of atmospheric disturbances, including atmospheric turbulence and particle scattering, on dynamic evolution of the femtosecond laser transmission filaments is numerically studied. The results show that atmospheric turbulence can cause the pulse shape to change in an irregular manner; in addition, atmospheric turbulence significantly affects the pulse energy flow during the self-focusing filamentation process. The attenuation of pulse energy can be attributed to particle scattering, thereby affecting the formation process of optical filaments. As the femtosecond laser travels through the cloud and fog, the length of the optical filament will decrease, the energy attenuation during the filamentation process will be accelerated, and the total deposited pulse energy will increase with the increasing particle number concentration and particle radius. The results presented here can provide some theoretical basis to evaluate the efficiency of the femtosecond laser related applications under real atmospheric conditions.