Two capacitors composed of ZnO nano-rods were fabricated with and without dielectrophoresis on two identical inter-digitated electrode arrays. Scanning electronic microscope images were presented to verify the aligned and not-aligned arrangement of the nano-rods. The capacitances were measured, and some marked improvements on the capacitor fabricated with dielectrophoresis were obtained. The capacitance value of the sample with dielectrophoresis is 2-3times larger than that of the sample without dielectrophoresis, and it has a better frequency independence, more excellent dc stability and lower dissipation factor between 30kHz and 5.3MHz. The influence of the arrangement of the optimal polarization directions on the capacitance is primarily discussed. The comparative results suggested that the ordered arrangement of the optimal polarization directions of the filling materials was expected to be employed potentially to regulate and control the capacitance during the fabrication process.