The present invention relates to a multiplex microfluidic device for selection of nucleic acid aptamers and a method for high-throughput selection of nucleic acid aptamers using the same, and more particularly to a multiplex microfluidic device (SELEX lap-on-a-chip) that uses an improved multiplex platform in place of the development of an aptamer for a single target and to a method for high throughput selection of aptamers using the same together with high-throughput sequencing. A multiplex microfluidic device according to the present invention can simultaneously detect aptamers for a plurality of targets, and it can greatly increase the screening throughput and greatly shorten the process time compared to conventional multiplex techniques. Particularly, when a process for selecting aptamers is performed using the device of the invention together with a high-throughput sequencing method, the number of target binding/elution/amplification rounds can be greatly reduced, and the process can be performed in an automated manner. Thus, the device of the invention is highly useful.