In order to clarify the relation between the current-voltage (I-V) characteristics of 3C-SiC Schottky barrier junctions (SBJs) and the defects in the epilayers, we have carried out the transmission electron microscope (TEM) observations, electron beam induced current (EBIC) measurement and Nomarski differential interference contrast microscopy (NDIC). We found that macro steps on the surfaces, which are originated from scratches on the substrate surfaces and twin bands, and stacking faults in the epilayers affect strongly on the reverse current characteristics of SBJs.