Microbial induced desaturation and precipitation (MIDP) has been proven to be an environmental-friendly and reliable method for liquefaction mitigation. This study further explored MIDP with yeasts that had better performance for soil desaturation. First, the growth characteristics of two kind of yeasts were analyzed. Then the gas production ability of yeasts was measured by drainage method. Finally, the shaking table test was conducted to investigate the liquefaction mitigation effect. The results showed that the yeast anaerobic gas production reaction can reduce the saturation degree of calcareous sand from 100% to 86.76%. In the shaking table test, bacterial solution of 4% sucrose content achieved the best desaturation effect, the saturation degree of the bottom layer could be reduced to 59.9%. The excess pore pressure ratio of the soil at the different depths had a decreasing trend. The change of soil shear wave velocity changes was tested after desaturation, and found that the shear wave velocity increased from 10 m/s to 70 m/s with a regularity as the saturation degree decreased. The results of this study provided a new perspective on yeast in calcareous sand desaturation.