The invention belongs to the field of polymer materials and bio-medical materials and particularly relates to a method for preparing chitosan/sodium alginate natural polymer core-shell microspheres by a one-step process. The method is characterized by comprising the following steps: firstly, preparing a calcium chloride/chitosan mixed solution and a sodium alginate solution; dripping the calcium chloride/chitosan mixed solution into the sodium alginate solution by use of a microinjector; placing to form microspheres; taking out the microspheres; and cleaning with distilled water to finally obtain the chitosan/sodium alginate natural polymer core-shell microspheres. The method has the advantages that the preparation process is simple, the preparation steps are simplified, the equipment is simple, the preparation conditions are mild, the control is easy, the repeatability is good, after-treatment is not needed, and the cost is low. The natural polymer materials which have the characteristics and advantages of being rich in source, green and environment-friendly, favorable in biocompatibility, non-toxic, biodegradable, and low in price are adopted as the preparation raw material, so that the prepared chitosan/sodium alginate natural polymer core-shell microspheres have a very high application value in the bio-medical field.