An novel on-chip synthesis technique for nanochannel arrays inside microfluidic channels is reported. The microfluidic channels are constructed with etched silicon trenches and a polydimethylsiloxane (PDMS) slab. These silicon microchannels provide a confined environment for highly oriented nanostructure synthesis. Triblock copolymer (SBA-15) is self-assembled inside the microchannel array as template for silica precursor polymerization under an induced temperature gradient. The temperature gradient is maintained by thermoelectric pads and used to control the direction and rate of organic solvent evaporation. This evaporation-induced self-assembly (EISA) process is confined within the microfluidic channels and guided into formation of highly ordered nanochannels with long range alignment. The fabrication and synthesis process is developed and the resultant nanomaterial is characterized. A fluorescent molecule dye, fluorescein, is used to demonstrate the potentials of the integrated device in nanofluidics applications.