We have investigated the electronic structure and transport properties of a pi-stacking molecular chain which is covalently bonded to a H/Si(100) surface, using the first-principles density functional theory approach combined with Green's function method. The highest occupied molecular orbital (HOMO) dispersion is remarkably reduced, but remains noticeable (similar to 0.1 eV), when a short pi-stacking styrene wire is cut from an infinitely long wire and sandwiched between metal electrodes. We find that the styrene chain's HOMO and lowest unoccupied molecular orbital (LUMO) states are not separated from Si, indicating that it does not work as a wire. By substituting -NO2 or -NH2 for the top -H of styrene, we are able to shift the position of the HOMO and LUMO with respect to the Fermi level. More importantly, we find that the HOMO of styrene-NH2 falls into the band gap of the substrate and is localized in the pi-stacking chain, which is what we need for a wire to be electrically separated from the substrate. The conductance of such an assembly is comparable to that of Au/benzene dithiolate/Au wire based on chemical bonding, and its tunability makes it a promising system for a molecular device.