Most studies on MnAs material in its bulk form have been focused on its temperature-dependent structural phase transition accompanied by a magnetic one. Magnetostructural phase transition parameters in thin MnAs films grown on substrates present however some differences from the bulk behavior, and local studies become mandatory for a deeper understanding of the mechanisms involved within the transition. Up to now, only surface techniques have been carried out, while the transition is a three-dimensional phenomenon. We therefore developed an original nanometer scale methodology using electron holography to investigate the phase transition in an epitaxial MnAs thin film on GaAs(001) from the cross-section view. Using quantitative magnetic maps recorded at the nanometer scale as a function of the temperature, our work provides a direct in situ observation of the inhomogeneous spatial distribution of the transition in the layer depth and brings new insights on the fundamental transition mechanisms.