In this paper, we report on stable liquid–air interfaces and high-aspect-ratio polymer micromembranes with complex and controlled structures formed within microfluidic channels. Selective alkanethiol treatment on gold and copper surfaces is employed to create hydrophilic–hydrophobic boundaries between glass and these metal surfaces within microchannels. Robust liquid–air interfaces, featured with different 3-D structures, are formed at these boundaries. The process for creating these liquid–air interfaces is highly reproducible. Simulations are conducted to further study the liquid–air interfaces. The liquid–air interfaces are then utilized for interfacial polymerization. Two immiscible liquid phases containing the reagents react and generate polymer micromembranes within microfluidic channels. Formed following the hydrophilic–hydrophobic boundaries, these membranes have not only complex footprints on the substrates but also different configurations in the $z$ -direction. Here, we demonstrate high-quality and complex 3-D nylon micromembranes fabricated in microchannels using this method.