As a nonthermal approach, microwave processing significantly enhances interface reactivity and preserves microchannel integrity during the bonding of poly(methyl methacrylate) (PMMA) microfluidic devices. By activating and aligning polymer chains at lower temperatures, this method promotes rapid bonding and improved interfacial adhesion, maintaining the precision of delicate microstructures essential for device functionality. Unlike thermal wafer bonding, which relies on elevated temperatures that may risk deforming delicate microstructures, the nonthermal effect of microwaves facilitates the activation and alignment of polymer chains at lower temperatures, enhancing interfacial adhesion through improved molecular interactions. Comprehensive experiments employing X-ray photoelectron spectroscopy and atomic force microscopy revealed that microwave treatment significantly improved the surface reactivity of PMMA, resulting in a bond strength that surpassed that of traditional methods without reaching the thermal degradation threshold. The rapid evaporation of isopropanol under microwave exposure minimizes thermal buildup, further demonstrating the contribution of nonthermal microwave effects to the bonding process. This approach represents a breakthrough in microfluidic device fabrication, balancing effective bonding with structural integrity, and holds significant promise for applications in biomedical engineering and MEMS.