To gain a high yield of xylooligosaccharides (XOS) at a low cost, W/W droplet-based microfluidic system combined with immobilized xylanase was constructed. Jetting-regime under the high viscosity of both two phases was correlated with the Ca and We numbers. W/W droplets were obtained with controllable sizes when the flow velocities of dispersed and continuous phases were in the range of 0.29–0.48 µL/min and 0.52–0.80 µL/min respectively. The droplet size could be expressed as a power-law relationship with the velocity ratio of two phases. The maximum yield of XOS was 75.0% within 10 min. Km value was reduced to a half compared with batch reactors. Xylanase-polymer conjugates were reused for 10 times, with a residual activity over 60%. The results confirmed that the combination of enzyme-polymer conjugates and W/W droplet-based microfluidic system is a low-cost and high catalytic efficiency method for biocatalysis.