The commissioning of the RPC-based muon detector in the BESIII experiment has been carried out. The RPC modules, front-end electronics, online and offline software of the muon system have been studied. The detector performances including efficiency, counting rate, noise ratio, spacial resolution, dark current, and muon charge ratio were obtained by cosmic ray data with and without magnetic field. The new operating high voltage and threshold were chosen after the scan experiment. The long-term stability of the BESIII RPCs made of bakelite without oil treatment was studied.