Graphene, a special two-dimensional material, has a unique band structure that allows the type and concentration of carriers to be controlled through a gate voltage, and it has potential applications in bipolar nanoelectronic devices. In this paper, based on the tight-binding model of graphene p-n junctions, by using the nonequilibrium Green’s function method and Landauer-Büttiker formula, the thermal dissipation of electric transport in graphene p-n junctions in a magnetic field is investigated. Under a strong magnetic field, both sides of the junction are in the quantum Hall regime, thus the topologically protected chiral edge states appear. Intuitively, the topologically protected chiral edge states are dissipationless. However, the results show that thermal dissipation can occur in the quantum Hall regime in graphene junctions in the presence of dissipation sources, although the topologically protected chiral edge states still exist. In clean graphene junctions, thermal dissipation occurs mainly at the edge for the unipolar transport, but it occurs both at the edge and at the interface of the junctions for the bipolar transport. In the presence of disorder, thermal dissipation is significantly enhanced both in the unipolar junction and in the bipolar junction, and it increases with disorder strength increasing. Besides, the energy distribution of electrons at different positions is also studied, which shows that the thermal dissipation always occurs as long as the energy distribution is in nonequilibrium. This indicates that the topology can protect only the propagation direction of electrons, but it can not suppress the occurrence of thermal dissipation.