High-temperature smoke generated by tunnel fires is the most important factor causing casualties. To explore the influence of natural wind on fire smoke movement in an extra-long highway tunnel based on the Taihang Mountain Tunnel, the distribution law of natural wind in the tunnel was obtained by on-site monitoring of the meteorological conditions at the tunnel site. A three-dimensional fire dynamics tunnel model considering an inclined shaft smoke exhaust was established, and the influence of natural wind on tunnel temperature distribution, smoke spread and smoke exhaust efficiency was studied. The results show that the natural wind speed of the Taihang Mountain Tunnel is mainly concentrated at 0~3 m/s. The main wind direction of the natural wind on the left tunnel is opposite to the driving direction, and the distribution probability of the main wind direction in each section is 81.27% and 72.15%, respectively. The main wind direction of the right tunnel is the same as the driving direction, and the distribution probability of the main wind direction in each section is 56.78%, 69.73%, 67.32% and 64.65%, respectively. The negative natural wind can inhibit the smoke spread downstream of the smoke exhaust port, but it is not conducive to the smoke exhaust. The positive natural wind promotes the smoke spread to the downstream of the smoke exhaust port, and the larger the natural wind speed, the longer the spread length. Natural wind reduces the smoke exhaust efficiency. For positive or negative natural wind with a guaranteed rate of 70%, the smoke exhaust efficiency is reduced by 27.76% and 15.59%, respectively, compared with the condition without natural wind. The research results can provide a useful reference for the design of fire smoke exhausts and smoke control schemes in extra-long highway tunnels.