A molecularly imprinted polymer nanoparticle (MIP) was prepared by integrating a mixed functional monomer into a highly cross-linked polymer. The nanosized insulin as a template transferred into the binding cavities, anchored functional monomer(s) that the insulin structure formed within free space of the molecular size region by MIP nanoparticles. The oral administration with the insulin-loaded MIP resulted in higher fluorescence intensity of rhodamine-labeled insulin into the epithelial cells. We observed the correlation between the lipophilic domains of dye over the affected areas of sites with the interplay of the intestinal epithelial layer on the different intestinal sections. And, the detection with guinea pig anti-insulin antibody followed by goat anti-guinea pig antibody clearly elicited the efficient insulin function in the necessary biological milieu. The root mean square roughness of the MIP indicated difference of the surface density, significantly lower compared with the polymer attributed to the protein-mucin uptake that efficiently promoted the insulin penetration. Eventually electron microscopy data of the conjugated biotin-gold nanoparticles showed the transport of insulin across the intestinal epithelium via transcellular pathway, and the development of the pancreatic β cell in the streptozocin-induced diabetic rats. Histopathological observation exhibited no obvious toxic effect after orally treated with MIP loaded insulin (100 mg/kg) daily for 14 days compared to control group. The use of an insulin-loaded MIP was proven to be an effective therapeutic protein delivery through transmucosal oral route.