In the present study, a low temperature and deformation-free bonding method to seal hydrophilicity-stable microchannels in polymethyl methacrylate (PMMA) microfluidic devices was proposed. Oxygen plasma pre-/post-treatments and polyvinyl alcohol (PVA) coating were performed on the PMMA microfluidic substrates before thermal bonding. Different surface treatments were characterized using a confocal profilometer, tensiometer, attenuated total reflection Fourier-transform infrared spectrometer (ATR-FTIR), differential scanning calorimeter (DSC), and scanning electron microscope (SEM). The effects of surface modification on bond strength and microchannel integrity were studied. Oxygen plasma treatment prior to PVA coating was found to be significant in improving the coating uniformity and enhancing the adhesion between the PVA layer and the PMMA base. The PMMA microchannel substrate could be bonded to a homogeneous PMMA cover plate at about 70 °C (30 °C lower than the PMMA glass transition temperature, T_g) with the coated PVA layer serving as a medium material which had high wettability, high surface energy and low T_g. With oxygen plasma post-treatment of the coated PVA layer, the bond strength was improved and comparable to that obtained by pure thermal bonding at a temperature near the T_g of PMMA. Due to the low bonding temperature, the microchannel integrity was well retained with negligible deformation. The hydrophilicity stability of different surface treatments was evaluated and compared under both dry and wet storage conditions for a month. The results suggested that the PVA-coated PMMA substrates with oxygen plasma post-treatment present the highest hydrophilicity and lowest hydrophobic recovery. As a demonstration, monodispersed oil-in-water (O/W) droplets with volumes of sub-10 nL were successfully and reliably generated in the hydrophilic microfluidic devices fabricated with the proposed bonding method.