Hybrid PEDOT:PSS-silicon heterojunction solar cells have the advantages of low temperature, low cost and solution process. However, as a low-quality native oxide layer can easily form on the surface of silicon substrates, the hybrid solar cells still suffer from charged carrier recombination at the defective interface, hence affecting the device characteristics. In this work, we employ a thermally induced silicon hydrosilylation technique to form a self-assembled monolayer(SAM) on the hydrogen-terminated silicon substrate, in order to prevent the oxidation and passivate the surface of silicon. The quality of this monolayer passivation is characterized by the contact angle, X-ray photoelectron spectroscopy (XPS) analyses. We have found that the SAM passivation can effectively reduce the contact resistance between silicon and the aluminum electrode, leading to an improved open-circuit voltage and fill-factor. However, as the silicon surface with the SAM passivation becomes hydrophobic, it is difficult to apply aqueous PEDOT:PSS solution onto silicon. Therefore, we further apply a low-damage oxygen plasma treatment to modify the terminal functional group of the monolayer to form a hydrophilic surface. The power conversion efficiency of the modified devices is between 10-12%. Although the PCE does not surpass the reference device due to possible chemical reactions between the PEDOT:PSS and SAM, the proposed low- damage oxygen-plasma treatment provide a viable solution for modifying the functional passivation of hybrid PEDOT:PSS silicon solar cells using SAMs.