The barrier potential profiles and microstructure of Co based magnetic tunnel junctions (MTJs) annealed up to 340℃ have been studied by electron holography (EH) and high resolution electron microscopy. The EH results reveal that the annealing process can well improve the quality of interfaces between barrier and ferromagnetic electrodes, and of AlOx barrier itself, which are responsible for the improvement of tunneling magnetoresistance in MTJs after anneal at 280℃.