The present disclosure discloses a three-dimensional integration system of an RFID chip and a supercapacitor and a manufacturing method thereof. The three-dimensional integration system of an RFID chip and a supercapacitor includes: a silicon substrate (200); an RFID chip (201) disposed on a front surface of the silicon substrate (200); a supercapacitor disposed on a back surface of the silicon substrate (200) at a position corresponding to the RFID chip (201), but not in contact with the RFID chip (201); through silicon via structures penetrating the silicon substrate (200) and respectively disposed on two sides of the RFID chip (201); wherein the RFID chip (201) has a chip positive electrode (2021) and a chip negative electrode (2022) electrically connected with a capacitor contact positive electrode (2131) and a capacitor contact negative electrode (2132) of the supercapacitor through the through silicon via structures on the two sides respectively; and a packaging substrate (218) electrically connected to the capacitor contact positive electrode (2131) and the capacitor contact negative electrode (2132).