The paper reports an island nucleation and secondary growth of aligned ZnO : Cu nanorod arrays via thermal vapor phase transport. Results analysis indicates that the secondary segment is epitaxially grown on the ZnO : Cu nanorods with the radius strongly dependent on temperature and the concentration of zinc vapor. The modified characteristic radius (R(c)) model is used to explain the nucleation and secondary growth process. Temperature-dependent photoluminescence spectra indicate that the band gap emission of the secondary growth nanorods is greatly restrained. A controversial 3.31 eV emission (A line) and two different donor-acceptor pair (DAP) recombinations at 3.24 eV and 2.48 eV are observed at 13 K. The A line shows a different behavior from the two DAP emissions during the heat-up process. Intrinsic room temperature ferromagnetism (RTFM) is observed in the secondary growth ZnO : Cu nanorods and it can be explained by oxygen vacancy and copper defects related to bound magnetic polar (BMP) or double exchange mechanism.