Non-erodible elements such as stones and vegetation are key to controlling wind erosion and dust emission in drylands. Stony deserts are widely distributed in the Gobi Desert, but the effect of stones on wind erosion and dust emission have not been well studied, except under artificial conditions. In this study, we evaluated the effect of stones on wind erosion and dust emission by measuring the sand saltation threshold in a stony desert in Tsogt-Ovoo in the Gobi Desert, Mongolia, under natural surface conditions during sand and dust storms. We quantified the amount of stones by measuring the roughness density, and determined the threshold friction velocity for sand saltation by measuring wind speed and sand saltation count. Our results showed that the threshold friction velocity increased with the roughness density of stones. In the northern part of the study area, where neither a surface crust nor vegetation was observed, the roughness density of stones was 0.000 in a topographic depression (TD), 0.050 on a northern slope (N.SL), and 0.160 on the northern mountain (N.MT). The mean threshold friction velocity values were 0.23, 0.41, and 0.57 m/s at the TD, N.SL, and N.MT sites, respectively. In the southern part of the study area, the roughness density values of stones were 0.000 and 0.070–0.320 at the TD and southern slope sites, respectively, and the mean threshold friction velocities were 0.23 and 0.45–0.71 m/s, respectively. We further compared the observed threshold friction velocities with simulated threshold friction velocities using Raupach's theoretical roughness correction and the measured roughness density values, and found that Raupach's roughness correction worked very well in the simulation of threshold friction velocity in the stony desert. This means that the results of our stone measurement can be applied to a numerical dust model.