Defects in hexagonal boron nitride (h-BN) play important roles in tunneling transport through the h-BN barrier. Here, using carbon-doped h-BN (h-BN:C) as a tunnel barrier containing defects in a controlled manner, we investigated tunneling transport through defects in the h-BN:C/graphene heterostructures. Defect-assisted tunneling through a specific kind of carbon-related defect was observed in all measured devices, where the defect level was always located at ∼0.1 eV above the graphene's charge neutrality point. We revealed a phonon-assisted inelastic process in the defect-assisted tunneling, in which carriers tunnel through the defect with phonon emission. Furthermore, when the h-BN:C barrier was thick (12 layers, ∼4 nm), sequential tunneling through two defects became dominant, where the phonon-assisted inelastic process shows substantial effects between the two defects. This study reveals the contribution of phonons to defect-assisted tunneling transport, which is essential for the development of defect-related van der Waals (vdW) electronic techniques.