Biomass resources, such as lignocellulose fermentation by industrial yeasts to produce various compounds including alcohol, ketone, aldehyde, and so on, contribute to solving non-renewable energy crisis. Thereinto, abundance and low price lignocellulose fermentation and environmentally friendly and energy efficient high gravity fermentation have attracted a lot of attention. However, inhibition of cell growth and metabolism by toxic compounds formed during pretreatment of lignocellulose, high concentration of substrate and product, osmotic stress, and elevating temperature, is a bottleneck problem in the fermentation industry. Here, we introduce the effect of osmolarity, temperature, and toxic compounds on cell growth, and review recent advances in stress tolerance mechanisms of industrial yeasts for these harmful factors at intracellular homeostasis, molecular level and so on.