The invention provides exenatide composite microspheres. The exenatide composite microspheres are characterized in that lecithin wraps exenatide and a protecting agent simultaneously, and after exenatide lipid nanoparticles are formed, a high-molecular polymer carrier encapsulates the exenatide lipid nanoparticles to prepare the exenatide composite microspheres; and the molecular weight of the high-molecular polymer carrier is 10000-90000, and the high-molecular polymer carrier is dissolved in a mixing organic solvent. The prepared composite microspheres are uniform in grain size, the encapsulation efficiency of the exenatide is high, the microspheres are spherical and have smooth surfaces, the mean grain size is between 1 mu m and 50 mu m, and by the characteristics of smooth surfaces, high encapsulation efficiency and uniform grain size, the releasing speed of the microspheres is stable, the microspheres can release for a long time, therefore, the drug-delivering frequency can be reduced, and the compliance of patients is good.