3D single-crystalline, well-aligned GaN-InGaN rod arrays are fabricated by selective area growth (SAG) metal-organic vapor phase epitaxy (MOVPE) for visible-light water splitting. Epitaxial InGaN layer grows successfully on 3D GaN rods to minimize defects within the GaN-InGaN heterojunctions. The indium concentration (In ∼ 0.30 ± 0.04) is rather homogeneous in InGaN shells along the radial and longitudinal directions. The growing strategy allows us to tune the band gap of the InGaN layer in order to match the visible absorption with the solar spectrum as well as to align the semiconductor bands close to the water redox potentials to achieve high efficiency. The relation between structure, surface, and photoelectrochemical property of GaN-InGaN is explored by transmission electron microscopy (TEM), electron energy loss spectroscopy (EELS), Auger electron spectroscopy (AES), current-voltage, and open circuit potential (OCP) measurements. The epitaxial GaN-InGaN interface, pseudomorphic InGaN thin films, homogeneous and suitable indium concentration and defined surface orientation are properties demanded for systematic study and efficient photoanodes based on III-nitride heterojunctions.