We present a new type of device to separate biochemical compounds wherein carbon nanotubes (CNTs) are integrated as chromatographic stationary phase. The CNTs were directly grown on the bottom of microfluidic channels on Si/SiO2 substrate by chemical vapor deposition (CVD). Acetylene was used as carbon source and Ni was employed as catalyst. For electrokinetic separations, higher electrical field strength is usually required; therefore, the CNTs were constructed in pillar-array-form by patterning Ni catalyst layer. Electrical field strength of 2.0 kV/cm has been realized, which is more than one order of magnitude higher than the one reported so far. The microfluidic chips integrated with CNTs were successfully used to separate a compound containing two Coumarin dyes, 240 mM C460 and 270 mM C480.