Cells residing in a microenvironment interact with the extracellular matrix (ECM) and neighboring cells. The ECM built from biomacromolecules often includes nanotopography. Through the ECM, interstitial flows facilitate transport of nutrients and play an important role in tissue maintenance and pathobiology. To create a microenvironment that can incorporate both nanotopography and flow for studies of cell–matrix interactions, we fabricated microfluidic channels endowed with nanopatterns suitable for dynamic culture. Using polymer thin film technology, we developed a versatile stitching technique to generate a large area of nanopatterned surface and a simple microtransfer assembly technique to assemble polydimethylsiloxane-based microfluidics. The cellular study showed that both nanotopography and fluid shear stress played a significant role in adhesion, spreading, and migration of human mesenchymal stem cells. The orientation and deformation of cytoskeleton and nuclei were regulated through the interplay of these two cues. The nanostructured microfluidic platform provides a useful tool to promote the fundamental understanding of cell–matrix interactions and may be used to regulate the fate of stem cells.