Thermal-annealing has been widely used in modulating the oxygen content of manganites. In this work, we have studied the effect of annealing on the transport properties and magnetoresistance of junctions composed of a La0.9Ca0.1MnO3+δ film and a Nb-doped SrTiO3 substrate. We have demonstrated that the magnetoresistance of junctions is strongly dependent on the annealing conditions: From the junction annealed-in-air to the junction annealed-in-vacuum, the magnetoresistance near 0-V bias can vary from ～-60% to～0. A possible mechanism accounting for this phenomenon is discussed.