Indium tin oxide (ITO) is a functional material with great transparency, machinability, electrical conductivity and thermo–sensitivity. Based on its excellent thermoelectric performance, we designed and fabricated a multilayer transparent microfluidic chip with multiple sets of on–chip heating, local temperature measurement and positive on–chip cooling function units. Temperature control plays a significant role in microfluidic approaches, especially in the devices that are designed for bioengineering, chemical synthesis and disease detection. The transparency of the chip contributes to achieve the real–time observation of fluid flow and optical detection. The chip consists of a temperature control layer made with an etched ITO deposited glass, a PDMS (polydimethylsiloxane) fluid layer, a PDMS cooling and flow control layer. The performances of the ITO on–chip microheaters, ITO on–chip temperature sensors and two coolants were tested and analyzed in different working conditions. The positive on–chip heating and cooling were proved to be area-specific under a large temperature–regulating range. This PDMS–ITO–glass based chip could be applied to both temporal and spatial stable temperature–regulating principles for various purposes.