A new class of multiply hydrogen-bonded heteroduplexes from readily available amidourea derivatives was designed, and their structures and selective assembling behaviors were investigated. Amidourea derivative 3 could selectively assemble with 1 to form a stable heteroduplex via eight intermolecular bifurcated hydrogen bonds, but could not assemble with 2 at all, because of their unique structures and the spacing effect, although 1 and 2 possessed the same hydrogen-bonding sequence. The high stability and selectivity will make the amidourea-based hydrogen-bonded heteroduplexes be potentially applicable in the design of well-defined supramolecular architectures and novel functional materials.