Abstract: In this paper,charge transportation in molecular junctions were investigated with a sandwich structure which consists of metal film/saturated alkanethiol self-assembled monolayers（SAM）/Au coated conducting-probe atomic force microscopy（CP-AFM）tip.Ⅰ-Ⅴcharacteristics of molecular junctions were measured.The experiment results showed that the molecular conductance decreases exponentially with molecule length,and tunneling was confirmed as the dominant transport mechanism in the saturated molecules.Rectification effect was also observed in this sandwich structure and theoretical analysis for this kind of rectification effect was given as well.