We investigate the effect of three types of intrinsic disorder, including that in pairing energy, chemical potential, and hopping amplitude, on the transport properties through the superconducting nanowires with Majorana bound states (MBSs). The conductance and the noise Fano factor are calculated based on a tight-binding model by adopting a non-equilibrium Green’s function method. It is found that the disorder can effectively lead to a reduction in the conductance peak spacings and significantly suppress the peak height. Remarkably, for a longer nanowire, the zero-bias peak could be reproduced by weak disorder for a finite Majorana energy splitting. It is interesting that the shot noise provides a signature to discriminate whether the zero-bias peak is induced by Majorana zero mode or disorder. For Majorana zero mode, the noise Fano factor approaches zero in the low bias voltage limit due to the resonant Andreev tunneling. However, the Fano factor is finite in the case of a disorder-induced zero-bias peak.