An exenatide-containing composition is in the form of microspheres, which are prepared by using exenatide acetate and polylactic-co-glycolic acid (PLGA) as raw materials, and the content of acetic acid in the prepared composition is lower than 0.01%. A method for preparing the exenatide-containing microspheres includes selecting a cleaning fluid of a proper external water phase and a proper amount to clean microspheres, and selecting a proper re-drying temperature to cure the microspheres after the microspheres are freeze-dried.