Ambipolar organic thin-film transistors based on a F16CuPc/α-sexithiophene p–n heterojunction have been fabricated and analyzed to investigate the temperature dependence of ambipolar mobilities. At high temperatures (>50 K), the ambipolar mobilities follow a thermally activated hopping process. Thermal activation energy (Ea) is 79.3 meV for n-channel and 60.9 meV for p-channel, larger than those of single-layer devices when the temperature exceeds 140 K. The increase in Ea appears to originate from the small ambipolar mobilities. At temperatures ranging from 50 to 140 K, we have a second regime with much lower Ea of 5.7 meV for n-channel and 4.6 meV for p-channel, where the charge transport is dominated by shallow traps. On the other hand, the ambipolar mobilities become practically temperature independent at temperatures lower than 50 K, which is described as bandlike transport.