Producing oligodextran with an enzymatic membrane reactor (EMR) is a promising alternative to traditional fermentation processes due to its high efficiency and environmental compatibility. Process analysis and optimization of an EMR system used for producing oligodextran are critical to improving EMR operating stability and cost effectiveness. We herein 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 the product quality and production efficiency. The optimal parameters of operating pressure and agitation speed for achieving high production efficiency depend on the selection of operating mode. EMR prefers higher operating pressure to increase the production efficiency under water feeding mode. However, since the membrane suffered severer fouling under substrate feeding mode, the extensive agitation is required to inhibit membrane fouling and enhance production yield. Our work paves a new avenue towards the fundamental understanding and designing of highly effective and low consumptive EMR for oligodextran production.