Polypyrrole (PPy) nanowires are widely used in supercapacitors due to their high faradaic pseudo-capacitance and specific surface areas. However, their rapid capacitance degradation is a key and broad issue that cannot be ignored. In this work, PPy/p-toluenesulfonate nanowires (PPy/pTS NWs) network films were electro-polymerized with different nanowire diameters (D) and film thicknesses (L). The effects of nanowire structure and the dissolved O2 (DO) in the media on the capacitance degradation behavior were investigated. With the cyclic voltammetry (CV) cycles increasing, the surface layer of PPy/pTS NWs was gradually damaged and dissolved with the loss of most doping anions, resulting in decreased specific capacitance. The high initial over-oxidation degree of PPy/pTS NWs and the high DO concentration significantly accelerated the degradation of PPy/pTS NWs during CV cycles. After the loss of most capacitance, PPy/pTS NWs network films were expanded with increased L but reduced D, displaying uniform degradation without fractured nanowires. The capacitance stability of PPy/pTS NWs could be enhanced by lowering the initial over-oxidation degree, inhibiting the loss of doping anions, and removing DO in the media.