To date, due to the low accessibility of enzymes to xanthan substrates, the enzymolysis of xanthan remains deficient, which hinders the industrial production of functional oligoxanthan. To enhance the enzymatic affinity against xanthan, the essential role of two carbohydrate binding modules- Mi CBMx and Psp CBM84, respectively, derived from Microbacterium sp. XT11 and Paenibacillus sp. 62047-in catalytic properties of endotype xanthanase Mi Xen were investigated for the first time. Basic characterizations and kinetic parameters of different recombinants revealed that, compared with Mi CBMx, Psp CBM84 dramatically increased the thermostability of endotype xanthanase, and endowed the enzyme with higher substrate affinity and catalytic efficiency. Notably, the activity of endotype xanthanase was increased by 16 times after being fused with Psp CBM84. In addition, the presence of both CBMs obviously enabled endotype xanthanase to produce more oligoxanthan, and xanthan digests prepared by Mi Xen-CBM84 showed better antioxidant activity due to the higher content of active oligosaccharides. The results of this work lay a foundation for the rational design of endotype xanthanase and the industrial production of oligoxanthan in the future.