Provided is a method of manufacturing a microfluidic channel with a membrane formed therein, the method including: preparing an apparatus for forming a membrane, the apparatus for forming the membrane including a first microfluidic channel, a second microfluidic channel being spaced apart from the first microfluidic channel, a bridge channel having a microchannel structure for communicating the first microfluidic channel and the second microfluidic channel with each other, and a control channel, which is partitioned by a gas permeable member from the bridge channel and through which gas flows; a fluid flowing operation in which a first fluid in a liquid state for moving first microparticles flows in the first microfluidic channel and a control gas in a gaseous state flows in the control channel; and forming a membrane having nanopores.