In this paper, unsteady flow and heat transfer of water flow in a backward-facing step under pulsating nanofluid blowing are studied numerically. Attention is focused to examine the impact of this type of blowing and its pertinent parameters on the heat transfer performance and to detect possible non-equilibrium between the base fluid and the nanoparticles inside the flow field. To this aim, the Eulerian-Eulerian two-phase model is adopted. This approach consists of separate equation sets for the base fluid and the nanoparticles. So, it provides details of the flow field for each of the constituents, separately. Computations are undertaken for different cases and the consequences of the frequency, amplitude, and the mean velocity of the pulsating blowing as well as the type, diameter, and the volume fraction of the nanoparticles therein on the heat transfer characteristics are analyzed. It is found that in addition to thermal conductivity of the blown nanoparticles, their penetration into the water flow is an important trait that has a momentous role on the heat transfer rate. In the current Eulerian-Eulerian simulation, temperature distributions of the base fluid and the nanoparticles are similar but the corresponding velocity fields are quite distinct. This reveals a kind of non-equilibrium between the base fluid and the nanoparticles inside the flow that invalidates equilibrium approaches (e.g., the single-phase model or the two-phase mixture model) for the description of the problem.