Chitooligosaccharides (COSs) with a degree of polymerization (DP)>3 are invaluable for functional foods, biomedicine and agriculture. However, controllable techniques for regulating the enzymatic process of chitosanase in preparing high-DP COS (HdpCOS) are not available currently. To control the preparation of HdpCOS, we constructed a continuous flow enzyme membrane reactor (EMR) based on a 10 kDa tangential flow membrane module with an intermittent enzyme replenishment mode in this study. This system made the real-time separation and controllable synthesis of HdpCOS during chitosan hydrolysis feasible. Using the number average molecular weight (Mn), product distribution, volumetric yield and production rate as the indicators, the effects of enzyme loading and residence time (RT) on the degradation process of chitosan were evaluated, and the preparation processes for COSs within different DP ranges were determined. The products were further separated and purified through ethanol precipitation, yielding HdpCOS with a predominant DP range from 8 to 13. The proposed EMR system exhibited operational simplicity and robust stability, demonstrating that it has potential for being used in the controllable production of COSs.