We demonstrate a novel technique to achieve a highly efficient terahertz (THz) modulation based on hybrid structures of organic layers (fullerene derivative [6,6]-phenyl-C61-butyric acid methyl ester (PCBM) and 6,13-bis(triisopropylsilylethynyl) pentacene (TIPS-pentacene) fabricated on both sides of a silicon (Si) substrate. The organic layer generating an optically induced electron (or hole) transfer is deposited on the back (or front) side of the Si substrate. The spatial charge separation improved owing to the transferred photo-excited electrons or holes at both interfaces of PCBM/Si and TIPS-pentacene/Si, enables a highly efficient THz wave modulation. The photoexcitation on the hole-transfer organic layer (TIPS-pentacene/Si) further improves the modulation efficiency, as the diffusion of electrons through the Si substrate is faster than that of photo-excited holes.