Herein, thermoelectric carbon nanoparticle (CNP)-carbon nanotube (CNT) heterostructures are introduced as a promising flexible thermoelectric material. The optimal barrier energy between the CNP and CNT increases the Seebeck coefficient (S) of the heterostructures through the energy filtering effect. For optimized thermoelectric performance, the CNP-CNT barrier energy can be effectively tuned by controlling the work function of the CNPs. The optimized p-type CNP-CNT heterostructures exhibited S and power factor (PF) of 50.6 ± 1.4 μV K-1 and 400 ± 26 μW m-1 K-2, respectively. The n-type CNP-CNT heterostructures, optimized for another work function of the CNPs, exhibited S and PF of up to -37.5 ± 3.4 μV K-1 and 214 ± 42 μW m-1 K-2, respectively. The energy harvesting capability of a thermoelectric generator prepared using p- and n-type CNP-CNT heterostructures with optimized barrier energies is demonstrated. The thermoelectric generator with 10 p-type and 9 n-type thermoelectric elements exhibited a maximum output power of 0.12 μW from a ΔT of 5 K. This work shows a facile strategy for synthesizing thermoelectric CNP-CNT heterostructures with optimized energy filtering effects. Application to the thermoelectric device on a paper substrate is also discussed.