Both well vertically aligned and uniformly separated (In)GaN nanorods (NRs) were successfully grown on Si(111) substrates by plasma-assisted molecular beam epitaxy. Effects of supplied indium (In) flux on the morphology of (In)GaN NRs were investigated systematically. The scanning electron microscopic analysis and transmission electron microscopic measurements revealed that the presence of In flux can help to inhibit NR coalescence and obtain well-separated (In)GaN NRs. By increasing the supplied In flux, the densities of (In)GaN NRs decreased and the axial growth rates increased. According to the energy dispersive X-ray spectrometry measurements and theoretical calculations, the increase of In content of the NRs enhanced Ga diffusion on the NR sidewalls, which resulted in an increased axial growth rate. A kinetic In-assisted growth model for the well-separated (In)GaN NRs is therefore proposed. The model explains that the presence of In flux not only reduces the density of (In)GaN NRs due to the increase in substrate surface migration of Ga adatoms at nucleation stage but also lead to a remarkable enhancement of axial growth rate at growth stage. Consequently, the NR coalescence was significantly suppressed. The results provide a demonstration of obtaining well-separated (In)GaN NRs and open up further possibility of developing (In)GaN NR-based optoelectronic devices.