In this paper, results of applying a non-uniform negative magnetic field on a ferrofluid (water and 3 vol.% Fe3O4) flow in a corrugated channel under constant heat flux boundary condition have been reported. The thermal behavior of the flow is investigated numerically using two phase mixture model and control volume technique. The commercial program Ansys-Fluent 12 has been employed as the numerical solver. It is concluded that using magnetic field with negative gradient on nanofluid flow in corrugated channels can be proposed as a suitable method to achieve higher heat transfer performance and augments the heat transfer coefficient and also reduces the wall temperature. This method can leads to design of more compact heat exchangers.