Microparticles have a wide range of applications in various areas. In this study, agarose microparticles (AGM) were successfully prepared by using a water-in-water (w/w) emulsification (WWEM) technique to eliminate the use of a surfactant. An aqueous agarose solution was employed as the dispersed phase, and polyethylene glycol (PEG) was used as the continuous phase. We evaluated how the characteristics of the microparticles were affected by different processing factors, including temperature, agitation speed, stirring time, concentration of agarose, and proportions of the two phases. The agarose microparticles obtained were nearly perfect spheres, and their particle sizes decreased with an increase in the agitation speed. Physicochemical characterization suggested that agarose microparticles, due to their ubiquitous stability, could be applied in most mild environments.