Studies of the deoxyribonucleic acid (DNA) molecule at surfaces are driven by both the inherent interest in understanding different aspects of this molecule and its importance in biomimetic materials science and molecular electronics. In this paper, we fabricate binary DNA/surfactant-modified DNA arrays on a heterogeneous patterned surface through twice controlled condensation and dewetting processes. Through the muCP technique, we created a hydrophobic/hydrophilic pattern, using a condensed microdroplet array as a template to fabricate a porous film of polystyrene (PS). With similarity to the "membrane-based patterning" method, this PS porous film was used as a mask, exposed hydrophilic regions inducing DNA to form as an array. After the PS porous films are peeled off, blocked surface sites emerged for the subsequent adsorption with other species. Through another condensation process, where a DNA aqueous solution droplet array could be used as a template, surfactant-modified DNA was sited in the ordered hydrophobic regions through a second dewetting process and hydrophobic interaction, and we fabricated binary arrays on the same surface. At the same time, the double-helical structure and function of DNA still remained. This provides a simple, flexible, and efficient patterning technique for biomolecules.