With fast development and high pace life in modern society, autoimmune diseases like inflammatory bowel disease had become increasingly common. Bu-Zhong-Yi-Qi-Tang (BZYQT), a famous traditional Chinese medicine prescription (TCMP), has been used for 700 years mainly in Eastern Asia countries for the treatment of gastrointestinal and respiratory disorder, and weakness after serious diseases. These diseases were proved to be closely related to human immune system, among which, mucosal immune system is the largest immune system. So it is necessary to discover the mucosal immune related bioactive components of BZYQT. To evaluate the mucosal immunomodulatory bioactivity of BZYQT and ingredients. Peyer's patches were collected from mice administrated orally with BZYQT, its related Octadecylsilane (ODS) fractions and polysaccharide part. Productions of several cytokines including IL-2, IL-4, IL-5, and IFN-γ from T lymphocytes were tested with enzyme linked immunosorbent assay (ELISA) by Peyer's patch cells ex vivo experiments. Chemical profile including low molecular part and polysaccharide part were investigated. Low molecular part of BZYQT and related ODS fractions were analyzed by ultra-performance liquid chromatography coupled with quadrupole time-of-flight tandem mass spectrometry (UPLC-Q/TOF-MS) based on LC-MS information from self-established compound library. exclusion chromatography, and chemical property has been analyzed. Three-days' administration of BZYQT enhanced productions of IL-4 and IFN-γ in T lymphocytes of Peyer's patches in addition to IL-2. Some hydrophobic low molecular weight fractions (30%, 70% and 100% MeOH ODS fraction), which were fractionated from BZYQT by ODS column chromatography, showed enhancing or suppressive effects on productions of IL-2, IL-4 or IL-5 in T lymphocytes of Peyer's patches after oral administration. Besides, 161 components from hydrophobic low molecular weight fractions of BZYQT were unequivocally identified or tentatively characterized by UPLC-Q/TOF-MS according to retention time behaviors and fragments, and most of them were flavonoids and saponins from Glycyrrhizae Radix, Citri Reticulatae Pericarpium, and Cimicifugae Rhizoma. Polysaccharide part was separated and purified both by anion-exchange and size. BZYQT also contained at least one neutral and three weakly or strongly acidic polysaccharides, and analysis of their chemical properties indicated that a neutral polysaccharide was glucan, and acidic polysaccharides possessed heteroglycan and pectic arabinogalactan features. Murine administration of polysaccharide fractions of BZYQT induced different changes on functions of T lymphocytes in Peyer's patches from hydrophobic low molecular weight fractions. By experiment using intranasally-immunized mice, BZYQT negatively regulated antibody response in lung as combinatorial actions of its low molecular weight ingredients and polysaccharides. BZYQT contains several low and macromolecular weight ingredients, which affect to immune-function of T lymphocytes in Peyer's patches, and the formula expresses its regulative activity on lower respiratory immune system through combinatorial actions of these ingredients on immunocompetent cells in Peyer's patches. Copyright © 2018 Elsevier B.V. All rights reserved.