This paper describes a charge pump system for a flexible thermoelectric generator (TEG). Even though the TEG has high-output impedance, the system controls the input voltage to keep it higher than the minimum operating voltage by modulating the input impedance of the charge pump using two-phase operation with low- and high-input impedance modes. The average input impedance can be matched with the output impedance of the TEG. How the system can be designed is also described in detail. A design demonstration was performed for the TEG with 400 Ω. The fabricated system was also measured with a flexible-type TEG based on carbon nanotubes. Even with an output impedance of 1.4 kΩ, the system converted thermal energy into electric power of 30 μW at 2.5 V to the following sensor ICs.