The alkali-soluble cell wall polysaccharides (CWPs), extracted from Nelumbo nucifera rhizome flour (NNRF), were treated with microwave radiation to modify their physical characteristics, functional properties, and antioxidant potential. The NNRF was treated at different levels of microwave treatment time (1, 2, 3, 4 and 5 min) using the low-medium intensity (200 W). The cell wall was isolated and CWPs were extracted in 10% KOH solution followed by their physical, functional, and antioxidant characterization. Microwave treatment resulted in the morphological, structural and compositional modifications in CWPs that were directly correlated with their functional properties and antioxidant potential. A significant (p < 0.05) time-dependent exponential decrease in extract yield, exponential increase in water holding, oil holding, and swelling capacities, a polynomial increase in iron-binding capacity, and a linear increase in antioxidant properties including Trolox equivalent total antioxidant activity, ferrous reducing power, and free radical scavenging capacity of microwave-treated CWPs was observed. The increase in the studied functional and antioxidant potential of the treated samples may be due microwave-induced exposure of hydroxyl groups and uronic acid residues in CWPs. The data would be a valuable contribution to the literature regarding microwave-induced modification in physical, functional and antioxidant properties of CWPs of N. nucifera rhizome.