Abstract This study aims to measure the flow field distribution in a microchannel with different heights adjusted. Two different materials, PDMS and Coverglass, were used to observe the flow velocity distribution change resulting from the difference in Zeta potential. The velocity distribution data were also obtained. In the experiment, 1¡Ñ TBE buffer solution with viscosity of 1 cp was used with the electric field intensity controlled under 5, 7.5 and 10 kV/m, respectively. Micrometer resolution Particle Image Velocimetry (£gPIV) was used to measure partial velocity distribution in order to explore the hydrodynamic stretch effect on DNA molecules when the microchannel, where the solution was placed, was adjusted to different heights. This study also statistically analyzed the stretch length distribution of DNA molecules in the microchannel and calculated the time of DNA molecule deformation and stress relaxation time in order to understand the stretch condition under different heights as well as the stretch and deformation of DNA molecules in microchannels.