This paper presents the magnetic properties of chrome ion (Cr+) implanted InxGa1−xN (x = 0.1, 0.3, 0.5 and 1.0) nanostructures grown by molecular beam epitaxy (MBE). The Cr+ implantation was conducted at 110 keV with three doses, namely 2.6 × 1015, 5.3 × 1015, and 1.3 × 1016 ions/cm2. The as-grown nanostructures exhibited diamagnetism before and after ion implantation without annealing. However, after annealing, the nanostructures exhibited ferromagnetism at room temperature. The saturation magnetization (Ms) and coercive force (Hc) increase with increasing Cr+ dose. The Ms of the InN nanorods with diameters of 100–160 nm is larger than that of those with small diameters of 60–80 nm. For InGaN nanostructures, the indium concentration—that is, the band structure—is more important than the diameters of the nanorods for the same doping level of Cr ions. The Ms of InGaN nanorods with an indium concentration of 10% reaches its maximum. The zero-field cooled (ZFC) and field-cooled (FC) curves show that nanostructures have no parasitic magnetic phases.