A series of polyaniline/carbon nanotube array (PANI/CNTA) composite electrodes are prepared by electrodeposition of PANI onto CNTA electrodes by 100–500 cyclic voltammetry (CV) cycles, with the aim to investigate the influence of microstructure on the capacitive performance of PANI/CNTA composites. The morphology of PANI/CNTA composites varies remarkably with the CV cycles of electrodeposition. The optimum condition is obtained for the PANI/CNTA composite prepared by 100 CV cycles, corresponding to the highest specific capacitance, best rate performance, and longest cycle life, which are much better than that of activated carbon fiber cloth, the PANI electrodeposited on stainless steel substrate, and CNTA electrode. The forming process of the microstructure and its influence on the capacitive performance of PANI/CNTA composites are presented in this paper.