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This paper describes a line-based microfluidic system for rapid and low-cost electrophoresis (CE) separation and electrochemical (EC) detection of ion samples. Instead of using liquid channel for sample separation, thin polyester threads of various diameters are used as the routes for separating the samples with electrophoresis. Hot-pressed PMMA chip with protruding sleeper structures are adopted to set up the polyester threads and for electrochemical detecting the ion samples on the thread. Plasma treatment greatly improves the wetability of thin threads and surface quality of the threads. The measured electrical currents on plasma treated threads are 10 times greater than the threads without treatment. Results indicate that nice redox signals can be obtained by measuring ferric cyanide salt on the polyester thread. The estimated detection limit for EC sensing of potassium ferricyanide (K3Fe(CN)6) is around 50 μM. Mixed ion samples of Cl-, Br- and I- are successfully separated and detected using the developed line-based microfluidic device.