<p><i>Sinojackia xylocarpa</i> is a rare endemic genus in China, and is endangered in their wild habitats. For endangered rare species, sexual propagation is significant for the protection of genetic diversity and restoration of wild population. Especially for <i>S</i>. <i>xylocarpa</i>, the artificially cultivated population is expanded by vegetative propagation, which could lead to a lack of diversity. The seeds of <i>S</i>. <i>xylocarpa</i> require stratification to germinate, during which the hard pericarp becomes soft, and endophytes and soil microorganisms are considered to be involved in the process. Amplicon sequencing was used to analyze the changes in microbial community structure and the role of microorganisms in pericarp degradation. Analyses of pericarp from fresh and stratified seeds of different stages revealed that the abundance of endophytic bacteria in pericarp presented an overall increasing trend during the stratification process; endophytic bacteria in stratified pericarp produce β-glucosidase to participate in the degradation of the pericarp. Soil fungal diversity analyses of different stages showed that the highest levels of the two samples of fungi function clustering is saprophytic in nutritional type; guild model also indicated that wooden saprophytic fungi abundance increased obviously; further the effect of degrading pericarp of four strains isolated from stratified pericarp are confirmed. The above results indicate that soil fungi are involved in degradation. The potential of microorganisms to break seed dormancy has been applied to endangered plants that face difficulties in germination, especially in their natural habitats.</p>