Nano-elastic microspheres are particle-absorbent polymers that can be applied in plugging water. They plug pores and throats, reducing the damage from water invasion. The plug effect and flow mechanism of nano-elastic microspheres during water invasion were investigated in this paper through laboratory experiments. The results of the plugging experiments show that the nano-elastic microspheres had a higher plugging rate and formed physical plugs in the aquiferous region, thus preventing water invasion. Online nuclear magnetic resonance experiments indicated that the nano-elastic microspheres migrated from large pores to smaller ones during the flow process, forming elastic plugs in the porous media. The nano-elastic microspheres expanded in the aquiferous layer, increasing the flow resistance through both physical and elastic plugging, thereby reducing the water cut. Nano-elastic microspheres employed physical plugging to prevent water invasion and exhibited elastic flow in the porous media during the invasion.