In this paper, we propose a novel and simple fabrication microchannel with parallelogram cross-section using anisotropic wet etching of Si wafer, and self-alignment between Si channel and PDMS mold. Single crystal Si wafer was used to fabricate microchannel and master for PDMS mold, using photolithography and anisotropic KOH etching. Si structure for microchannel and master were formed on the same Si wafer by KOH etching, and the PDMS mold was made from Si master. Thus, we could fabricate the Si microchannel and PDMS mold, with same structural height. Finally, a microchannel with parallelogram cross-section could be easily formed, through self-alignment between them. Si microchannel and PDMS mold were permanently bonded, using O₂ plasma treatment. It is expected that the fabricated microchannel with parallelogram cross-section, can be used to study inertial focusing, widely used to separate particles continuously and with high-throughput.