Patulin (PAT), a toxic fungal metabolite, can directly damage the intestinal barrier and gut homeostasis via altering microbiota composition. Although there are several attempts for the control of PAT in vitro, there are currently few studies on the improvement of intestinal damage caused by patulin using in vivo assay. In this study, a nanoparticle formulation of spherical bacterial cellulose was obtained by dynamic fermentation of Acetobacter xylinum to prepare bacterial cellulose nanoparticles (BCNs) and then modified with 3-mercaptotetraethoxysilane to produce BCN(SH), to increase PAT adsorption in vitro. Meanwhile, results revealed that BCN(SH)s protected the small intestinal microbial barrier and can be used by microorganisms, such as Bacteroides, Firmicutes, and Actinomycetes, to produce short-chain fatty acids (SCFAs). BCN(SH)s appears as a promising edible material that can be used to alleviate intestinal damage from patulin, and has yet to be tested in other gut intoxication models.