Naturally occurring nanoscale exopolysaccharide (EPS) has attracted much attention in recent years. In this research, we obtained a new kind of naturally occurring spherical EPS nanoparticles (EPS-R503) from Lactobacillus plantarum R503. The secretion, self-assembly process, morphological structure, and surface characteristics of the as-prepared nanoparticles were comprehensively revealed with transmission electron microscopy (TEM) and atomic force microscope (AFM) for the first time. It was found that the EPS-R503 nanoparticles consist of negatively charged heteropolysaccharide composed of mannose, glucose, galactose, and glucuronide with several functional groups including -OH, -COOH, and -NH2. When different solvents were used to treat the EPS-R503 nanoparticles, the morphological structure and surface properties could be changed or manipulated. The forming mechanism of EPS-R503 was elucidated based on the aggregation processes from a fundamental point of view. Furthermore, EPS-R503 can serve as reducing and stabilizing agents for the biosynthesis of manganese dioxide nanosheets (MnO2 NSs), leading to EPS-MnO2 nanocomposite. The as-prepared nanocomposites can absorb fluorescein (FL) to form EPS-MnO2-FL, which can be used to detect glutathione (GSH) with a low limit of detection (0.16 μM) and a wide detection range from 0.05 to 4 mM. The excellent biocompatibility of EPS-MnO2-FL endows the feasibility of in vivo detection of GSH as well. Overall, the findings from this work not only benefit the exploitation of naturally occurring EPS nanomaterials but also provide a novel strategy for the green synthesis of metal-containing nanosheets for GSH detection.