This paper presents a new application of atmospheric pressure plasma jet (APPJ) aiming for fabricating a microfluidic system on a polydimethylsiloxane (PDMS) surface. While PDMS is widely used for microfluidic chips, the fabrication of a chip requires different instruments which are not easily accessible for small-scale companies or laboratories. Therefore, we are motivated to develop a simple and low-cost method for such a fluidic system fabrication. The idea of this work is to directly pattern a fluidic channel on a PDMS surface with a plasma jet, which is known for its capability of modifying the hydrophobicity on a surface. The feasibility test first showed that fluid only flows in plasma-treated regions as having physical walls. The plasma parameters were then optimized using Taguchi method based on experiments. The optimization significantly reduce the required plasma treating time from more than 30 treating rounds to only 3 treating rounds, over ten times improved. Methods for further improving the resolution to micrometer-scale have been discussed. In addition to the advantages of fast and low-cost of the proposed method, making microfluidic channels on the surfaces of PDMS chip is also convenient for recollecting cultured cells on a chip in the field of regenerative medicine.