Capillary electrophoresis chip has gradually ripe along with the development of MEMS technology. However, such these electrophoresis chips was design closed-channel form whose process including the micro-channel forming and chip bonding and so on, so the cost is higher. In addition, if these chips use repeated will cause some pollution problems such as obstruction or difficult to clean in the closed-channel. Therefore, to fabricate a non-closed microfluidic chip system will resolve the issues above listed. In this study has successful developed a convenient and low-cost thread microfluidic system, the thin polyester thread is instead of the traditional closed separation channel. And to avoid the cross contaminations that the separation channel can free replace a new electrophoresis separation channel by the roller equipment. Thread microfluidic systems can take advantage of capillary action to move, as a disposable chromatography flow channel, and the electric field is applied to this system for electrophoresis separation and electrochemical detection in the backend. This research develop an novel process technology, the hot embossing technology shape from concave embossing and metal coating procedure in PMMA, the salient pillow-electrode structure has be produced in PMMA board, the salient electrode structure set up the polyester fiber thread, the polyester fiber thread is as the electrophoresis separation channel, and electrochemical detect samples in back-end. In this study take plasma treatment to improve wettability and surface roughness of the polyester fiber thread, in order to improve the operational effectiveness of the thread microfluidic systems. The cyclic voltammetry measure potassium ferricyanide samples and the results showed that the performance of thread microfluidic system significantly increase after the plasma treatment, the measuring current value is 10 times greater than without the plasma treatment, and the estimated detection limit of potassium ferricyanide is around 6.25 £gM in the plasma treatment one. In addition, the thread microfluidic devices with plasma treatment has successful separation and detection the mixing samples of 0.3 mM chlorine, bromine and iodine ions, and the signal of the S/N ratio is 6 times higher than the without plasma treatment one, and the number of theoretical plates of electrophoresis separation also enhance to 28% in the plasma treatment one. In addition, in order to further enhance the detection sensitivity of the thread microfluidic systems, the study design and fabricate the concave-shaped three-dimensional electrode structure, and to achieve greater contact area between thread and the electrode. Thread microfluidic system with plasma treatment detect in concave-shaped three-dimensional electrode and flat electrode respectively, the results showed that concave-shaped electrodes in the potassium ferricyanide detection limit that measured current value is 10 times greater than flat electrode, and a mixture of dopamine and catechol sample are electrophoresis separated that concave-shaped 3D electrode whose measured S/N ratio is 5 times higher than flat electrode, and the number of theoretical plates is 1.5 times higher than the flat electrode. This study develops a novel thread microfluidic system that will provide a simple process and low-cost, and can solve the shortcomings of conventional closed-channel electrophoresis chips. In future, in this study develop the thread microfluidic system architecture will have contribute for fast electrophoresis separation and detection.