There are many studies on hydrogel microspheres due to their good biocompatibility and tunable physicochemical properties. This mini review summarizes the synthesis methods and applications of various functional hydrogel microspheres. The common preparation techniques of hydrogel microspheres are first briefly introduced, including emulsion polymerization, microfluidics, photolithography, electrospray and 3D printing. Besides, the related research progress of hydrogel microspheres in various fields was reviewed and focused on the application of hydrogel microspheres as delivery platforms, enzyme immobilized microcarriers, antibacterial agent and some new fields. Finally, the limitations and future prospects of the development of hydrogel microspheres were presented. It is hoped that this review can provide a beneficial reference for the development of hydrogel microspheres and foster the application in a wider range of fields.