After a long evolution, plants have developed biomass recalcitrance to make the resistance to microbial and enzymatic deconstruction. In order to make conversion of biomass more effective, pretreatment is a necessary and effective process. pretreatment technique can remove hemicellulose and lignin from the substrate and significantly increases the accessibility of the substrate. However, natural biomass is made up of different kinds of cells and organ, which means the substrate has heterogeneity in physical properties and chemical properties, and therefore, pretreatment of the same condition is difficult to sufficiently and properly treat all components. As a result, the pretreatment of one certain component is insufficient, and for some of the easily reactive portions, the same pretreatment is excessive, which leads to problems such as a large amount of inhibitors in the substrate or loss of sugar degradation. These factors, which are produced by pretreatment to inhibit subsequent enzymatic hydrolysis or fermentation, are summarized as biomass second recalcitrance. In this review, the reasons for biomass second recalcitrance production were analyzed and steam explosion technology was took as an example to explain a series of strategies to overcome the biomass second recalcitrance.