One-dimensional conducting polymer nanostructure arrays could provide short ion transport paths, thus delivering superior chemical/physical performance and having large potential as intelligent switching materials. In this work, in situ electrochemical atomic force microscopy is employed to monitor the self-assembly of conducting polypyrrole nanotube arrays in template-free electrochemical polymerization. The specific spreading behavior of pyrrole micelles on the conductive substrate is important to large-area self-assembly of conducting polypyrrole nanotube arrays and the insight into self-assembly of conducting polypyrrole nanotube arrays is discussed. Moreover, compared with unoriented nanostructured polypyrrole, the conducting polypyrrole nanotube arrays possess enhanced electrical and electrochemical performances.