In this paper, glucose oxidase (GOx) was employed to construct a functional film on the poly(dimethylsiloxane) (PDMS) microfluidic channel surface and apply to perform electrophoresis coupled with in-channel electrochemical detection. The film was formed by sequentially immobilizing poly(diallyldimethylammonium chloride) (PDDA) and GOx to the microfluidic channel surface via layer-by-layer (LBL) assembly. A group of neurotransmitters (5-hydroxytryptamine, 5-HT; dopamine, DA; epinephrine, EP; dobuamine, DBA) as a group of separation model was used to evaluate the effect of the functional PDMS microfluidic devices. Electroosmotic flow (EOF) in the modified PDMS microchannel was well suppressed compared with that in the native one. Experimental conditions were optimized in detail. As expected, these analytes were efficiently separated within 110 s in a 3.7 cm long separation channel and successfully detected at a single carbon fiber electrode. Good performances were attributed to the decreased EOF and the interactions of analytes with the immobilized GOx on the PDMS surface. The theoretical plate numbers were 2.19 Â 10 5 , 1.89 Â 10 5 , 1.76 Â 10 5 , and 1.51 Â 10 5 N/m at the separation voltage of 1000 V with the detection limits of 1.6, 2.0, 2.5 and 6.8 mM (S/N ¼ 3) for DA, 5-HT, EP and DBA, respectively. In addition, the modified PDMS channels had long-term stability and excellent reproducibility.