A super-layer deposition method is developed for 3D macroscopic finite element modeling of heat transfer at part scale during the powder bed fusion (PBF) process. The proposed super-layer strategy consists of the deposition of batches of several layers. The main consideration is to deal with the effective heating times and with the inter-layer dwell time in a reasonable way. The material is deposited at once for each super-layer thanks to level set and mesh adaptation methods, while the energy input is prescribed, either by respecting the layer-by-layer thermal cycle or in a single thermal load. The level set method is used twice: first to track the interface between gas and the successive super-layers of powder bed and second to track the interface between the part in construction and the nonexposed powder. To preserve simulation accuracy, adaptive remeshing is used to maintain a fine mesh near the evolving construction front during the process. Simulation results obtained by means of this super-layer method are presented and discussed by comparison with those obtained by layer-by-layer strategy, considered here as a reference. It is shown that, when respecting certain conditions, temperature evolutions and distributions approaching the reference ones can be obtained with significant savings on computation time. Assessment is first performed on simple part, then on a more complex configuration.