The improper discharge of industrial wastewater causes severe environmental pollution and the textile industry’s dye usage contributes significantly to industrial wastewater pollution. Hence, an effective method for removing the harmful substance methylene blue (MB) from dye wastewater is proposed. This method adopts a three-dimensional graphene composite material based on manganese dioxide (MnO2), named polyurethane@ reduced graphene oxide@ MnO2 (PU@RGO@MnO2). First, graphene is prepared with hydrazine hydrate as a reducing agent and polyurethane as a framework. MnO2 nanoparticles are synthesized by the reaction of potassium permanganate (KMnO4) with carbon. These nanoparticles are then loaded onto the three-dimensional framework to create the composite material. Finally, adsorption and removal experiments for MB are conducted to compare the performance of the composite material. The results indicate that the graphene based on the polyurethane framework exhibits favorable mechanical properties. The unique three-dimensional lattice structure provides abundant active sites for loading MnO2 nanoparticles, significantly increasing the contact area between the adsorbent and MB solution and thus improving the adsorbent utilization rate (reaching 94%). The nanoparticles synthesized through the reaction of KMnO4 with carbon effectively suppress the agglomeration phenomenon. Additionally, the introduction of dynamic adsorption and dynamic removal modes, aided by a water pump, substantially enhances the adsorption and removal rates, showcasing excellent performance. The research on a multi-porous three-dimensional structure holds significant practical value in water treatment, offering a new research direction for dye wastewater treatment.