This paper presents the fabrication of the micro fluidic platform for microfluidic encapsulation in Ca-Alginate microspheres toward the whole-cell neutralizing system for PEDV. This system has become a valuable antigen surface exposing tool for a broad spectrum of vaccine development and therapeutic applications. PED viral epitope regions (ER-1 and ER-2) were successfully expressed on the surface of yeast and their fluorescent activity was observed. Ca-alginate microspheres with encapsulated yeast were successfully produced using the fabricated micro fluidic platform and verified through the microscopic observation of the fluorescent-stained yeast cells in the microsphere.