Multiple gastrointestinal barriers (mucus clearance and epithelium barrier) are the main challenges in the oral administration of nanocarriers. To achieve efficient mucus penetration and epithelial absorption, a novel strategy based on mesoporous silica nanoparticles with dendritic superstructure, hydrophilicity, and nearly neutral-charged modification was designed. The mPEG covalently grafted dendritic mesoporous silica nanoparticles (mPEG-DMSNs) had a particle size of about 200 nm and a loading capacity of up to 50% andrographolide (AG) as a nanocrystal cluster in the mesoporous structure. This dual strategy of combining with the surface topography structure and hydrophilic modification maintained a high mucus permeability and showed an increase in cell absorption. The mPEG-DMSN formulation also exhibited effective transepithelial transport and intestinal tract distribution. The pharmacokinetics study demonstrated that compared with other AG formulations, the andrographolide nanocrystals-loaded mPEG-DMSN (AG@mPEG-DMSN) exhibited much higher bioavailability. Also, AG@mPEG-DMSN could significantly improve the in vitro and in vivo anti-inflammatory efficacy of AG. In summary, mPEG-DMSN offers an interesting strategy to overcome the mucus clearance and epithelium barriers of the gastrointestinal tract.