In this report, a solvent bonding method based on phase-changing agar hydrogel has been developed for the fabrication of poly(methyl methacrylate) (PMMA) microfluidic chips. Prior to bonding, the channels and the reservoir ports on PMMA channel plates were filled with molten agar hydrogel that could gelate to form solid sacrificial layers at room temperature. Subsequently, PMMA cover sheets were covered on the channeled plates and 1,2-dichlororethane was applied to the interspaces between them. The agar hydrogel in the channels could prevent the bonding solvent and the softened surface of the PMMA cover sheets from filling in the channels. After solvent bonding, the agar hydrogel in the channels and the reservoir ports was melted and removed under pressure. The sealed channels in the complete microchips had been examined by an optical microscope and a scanning electron microscope. The results indicated that high-quality bonding was achieved at room temperature. The prepared microfluidic microchips have been successfully employed in the electrophoresis separation and detection of three cations in combination with contactless conductivity detection.