c-oriented Co-doped ZnO （Zn0.96Co0.04O） thin films have been grown on the a-plane and c-plane sapphire substrates using molecular-beam epitaxy, respectively. In contrast to single crystalline Zn0.96Co0.04O film grown on a-plane sapphire, the film grown on c-plane sapphire were found to be twin-crystalline; some domains have a 30° rotation to reduce the large mismatch. The presence of these rotation domains in the twin-crystalline ZnO thin film causes much more carrier scattering at the boundaries, leading to much lower mobility and smaller mean free path of the mobile carriers, as compared with those of the single crystalline one. X-ray absorption fine structure studies revealed that most Co ions were in divalent state and actually substituted into ZnO lattice without formation of any detectable secondary phase. As compared with just a small saturation moment in the single crystalline Zn0.96Co0.04O thin film, the much stronger ferromagnetism in the twin-crystalline one indicates that the ferromagnetic origin should be highly correlated with structural defects in the twin-crystalline film. The possible magnetic mechanisms were discussed.