In this study, we propose a novel and simple fabrication method of the microfluidic device, with high-aspect-ratio (HAR) microchannel for microparticle separation under viscoelastic fluid flow. To fabricate the HAR (> 10) microfluidic device comprised of the Si channel and PDMS mold, basic MEMS processes such as photolithography, reactive ion etching and anisotropic wet etching of Si wafer were used, and then plasma bonding with mechanical alignment between the Si channel and PDMS mold was conducted. The width of the microchannels was determined by the difference between the Si channel width and the master width for the PDMS mold. On the other hand, the heights of the Si channel and PDMS mold could be controlled by the KOH etching time and spin-coating speed of SU-8, respectively. The HAR microfluidic device whose microchannel had 10 μm width and 100 μm height was successfully fabricated, and used to separate microparticles without other external forces. The effect on the particle focusing position and focusing width under viscoelastic fluid was investigated, depending on the flow rate and the microparticle size. It is expected that precise manipulation as well as high-throughput separation of microparticles, can be achieved using the microfluidic device with HAR microchannel.