Disclosed are a microfluidic device for isolating targets from a sample and a method for isolating targets using same. The microfluidic device of the present invention comprises a case, a first capture array, and a second capture array. The case has a channel formed therein, the channel having an inlet for introducing a sample having a plurality of different types of targets, and an outlet for discharging the sample. The first capture array is provided upstream of the channel, and includes a plurality of first funnels arranged along the direction orthogonal to the flow direction of the sample so as to capture the plurality of different types of targets. The second capture array is provided downstream of the first capture array, and includes a plurality of second funnels arranged along the direction orthogonal to the flow direction of the sample so as to capture the plurality of different types of targets. The targets captured on the first and second funnels are discharged to the outside of the case and collected by turning over and positioning the case and supplying a solution thereto.
