In GaN micro-rods, phase separation of the AlGaN electron-blocking layer is an enormous obstacle for achieving high-efficiency light-emitting diodes, as this phenomenon negatively affects the device efficiency by inducing unwanted band-energy modulations. Here, we found that the AlGaN electron-blocking layer on each m-plane of the GaN micro-rod appears to be phase separated, and each electron-blocking layer has a different thickness and length. Our careful analysis based on atom probe tomography reveals that the Al distribution in AlGaN is not uniform and that Al-rich and Al-deficient regions are clearly present. In addition, the longer surface diffusion length of Ga adatoms, as compared to Al adatoms, and the different initial strain state of each m-plane in the GaN rods are deeply associated with the different growth rate and inhomogeneous Al composition of AlGaN, resulting in phase separation of the AlGaN electron-blocking layer. These atomic-scale observations in the structural and chemical composition of AlGaN grown on GaN micro-rods could provide expanded opportunities for building a wide range of high-quality AlGaN electron-blocking layers.