To evaluate the electrical performance of molecularly modified metal-semiconductor diode junctions, organic monolayers were grafted on both hydrogen-terminated and oxidized silicon (p-type) surfaces. Three model systems, i.e., Hg\C12H25Si, Hg\SiO2-Si, and Hg\C12H25SiO3-SiO2-Si, were prepared and systematically , characterized based on their current-voltage and capacitance-voltage properties. The experimental results showed that mercury-silicon junctions modified with n-dodecyl monolayer display better rectifying behavior, i.e., larger rectifying ratio and smaller empirical ideality factor (i.e., close to unity), than those passivated with SiO2 thin films and n-dodecylsiloxane monolayers (formed on oxidized silicon). The differential capacitance measurements revealed that organic modified junctions (both alkylated and alkylsilated samples) have substantially lower densities of interface states in comparison with that of Hg\SiO2-Si. This work provides a clear assessment of the varied device performance among differently prepared metal-molecule-semiconductor junctions, which is complementary to the topic studies on the electron transport across these molecular interfaces. More importantly, the present research augments the potential applications of molecular modification and surface engineering in the fabrication of silicon-based microelectronic devices.