The low solubility, gel strength and shear resistance of waxy rice limit utility in large-scale and widespread food applications. Herein, functional properties of waxy rice starch (WRS) have been improved through sequential branching enzyme (BE) and glucoamylase (GA) treatment with wheat amylose (WA), rice amylose (RA) and corn amylose (CA) as the substrate. The results suggest that, compared to the BE treatment, the sequential GA→BE treatment significantly improves the WRS properties. Among the three substrates, WA appears to be suited highly for the WRS through the GA→BE treatment. GABE-WRS/WA had the highest content of α-1,6-glucosidic linkages, increased number of short chains, shortest average chain length, increased crystallinity, enhanced solubility, paste clarity and swelling power, elevated gelatinization temperature and enthalpy, increased viscosity, strongest gels, and highest shear-resistance. Overall, the sequential GA→BE treatment appears to be suitable to modify the functional properties of waxy rice starch toward developing more palatable and large-scale food products.