Conformational control of macromolecules is useful for efficient chemical and biochemical reactions. This paper reports a conformational control method for macromolecules, such as long-strand DNA, in microchannel flow, along with a simple method to stretch DNA strands by microfluidics. Stretching and orientation of DNA molecules by control of flow within a microchannel was directly observed by optical microscopy. This technique is useful to create chemical reactions with macromolecules; it offers high selectivity and efficiency that are impossible to achieve in bulk solution. We also demonstrated that our microfluidic stretching method can accomplish efficient hybridization of long-strand DNA.