Single-crystalline hyperbranched nanostructures of iron hydroxyl phosphate Fe5(PO4)4(OH)3·2H2O (giniite) with orthorhombic phase were synthesized through a simple route. They have a well-defined dendrite fractal structure with a pronounced trunk and highly ordered branches. The toxicity test shows that the hyperbranched nanostructures have good biocompatibility and low toxicity level, which makes them have application potentials in life science. The study herein demonstrated that the obtained hyperbranched giniite nanostructures show highly selective capture of phosphopeptides and could be used as a kind of promising nanomaterial for the specific capture of phosphopeptides from complex tryptic digests with the detection of MALDI-TOF mass spectrometry.