Far infrared (IR) radiation was employed in the embossing and bonding of poly(methyl methacrylate) (PMMA) microfluidic chips owing to its high penetration ability and heating efficiency. To emboss a channel plate, a piece of PMMA plate was sandwiched between a template and a glass plate. They were exposed to IR radiation for 5 min at 130 °C under pressure in a far IR-assisted embossing/bonding system. Subsequently, the embossed channel PMMA plate was bonded with a PMMA cover plate with the aid of far IR radiation and pressure. Satisfactory bonding could be achieved within 3 min at 100 °C. The fabricated microchips were successfully employed in the electrophoretic separation of four nitroaromatic compounds. Far IR-assisted embossing and bonding approaches indicate great promise for the mass production of PMMA microchips at low cost and should find a wide range of applications.