Process analysis and optimization of an EMR system used for producing oligodextran are critical to improving EMR operating stability and cost effectiveness. We developed a mathematical model to evaluate the effects of operating conditions and membrane properties on the reaction-separation behavior of an EMR. Our analysis shows that tailoring a membrane with large porosity and uniform pore size distribution can simultaneously improve product quality and production efficiency. The optimum parameters of operating pressure and agitation speed depend on the selection of operating mode. A higher operating pressure was preferable for increasing the production efficiency of the EMR system under a water feeding mode. However, since the membrane suffered more severe fouling under a substrate feeding mode, extensive agitation was required to inhibit membrane fouling and enhance production yield. Our work paves the way for a new approach towards design of highly effective and low-consumptive EMR systems for oligodextran productio