Self-assembled GaN nanorods were grown by metal-organic chemical vapor deposition. A highly regular rosette-shaped cathodoluminescence pattern in the GaN nanorods is observed, where its origin is helpful to deepen the understanding of GaN nanorod growth. The pattern forms at the very early stages of nanorod growth, which consists of yellow luminescence at the edges and the non-luminous region at six vertices of the hexagon. To clarify its origin, we carried out detailed cathodoluminescence studies, electron microscopy studies and nanoscale secondary ion mass spectrometry at both the nanorod surface and cross-section. We found the pattern is not related to optical resonance modes or polarity inversion, which are commonly reported in GaN nanostructures. After chemical composition and strain analysis, we found higher carbon and nitrogen cluster concentration and large compressive strain at the pattern area. The pattern formation may relate to facet preferential distribution of non-radiative recombination centers related to excess carbon/nitrogen. This work provides an insight into strain distribution and defect-related emission in GaN nanorod, which is critical for future optoelectronic applications. [Figure not available: see fulltext.].