The purpose of this study was to formulate nanoparticles with an elaborate structure for oral delivery of exendin-4 using a simple preparation process. The nanoparticles possessed a mixed lipid shell and an aqueous core which contained drug-loaded micelles. Formulation was optimized by a central composite design and the structure of the nanoparticles was validated. The efficacy for delivery of exendin-4 was evaluated both in vitro and in vivo. The drug encapsulation efficiency of the nanoparticles reached 97.7%. The nanoparticles greatly enhanced the cellular uptake and transport of encapsulated exendin-4 in vitro. The in situ study showed that exendin-4 could be transported across the epithelium into intestinal capillaries, while the lipid materials largely remained in the epithelium. Pharmacodynamic studies in diabetic KKAy mice demonstrated that the exendin-4-loaded nanoparticles exhibited a marked hypoglycemia effect with a pharmacological availability of 12.7% after intestinal administration.