Low-resistance magnetic tunneling junctions consisting of Ta/NiFe/Cu/NiFe/IrMn/CoFe/Al (6.6 and 7.7 A)-oxide/CoFe/NiFe/Ta were fabricated with the plasma-oxidized insulation layer. Electrical properties and microstructure of the junctions are characterized before and after annealing the junction at temperatures up to 300 C. While the Al (7.7 A)-oxide junction showed a continuous increase in the magnetoresistance (MR) ratio, reaching the maximum of 48% at 300 C, the Al (6.6 A)-oxide junction showed a moderate enhancement at 250 C and then a sharp drop in the MR ratio at 275 C. Transmission electron microscopy revealed, prior to the heat treatment, rough interfaces at the insulation layer. The annealing process made the oxide interfaces sharper, but also caused microstructural alteration of the bottom electrode. While the smoother oxide interface appears to be beneficial to the TMR effect, the Al (6.6 A)-oxide junction was susceptible to the localized short-circuiting of the electrodes and the thermal treatment would promote such shortcircuiting leading to the marked drop in the MR ratio. We have shown that the thermal treatment of the multi-layer tunnel junctions can either enhance or degrade the electrical properties depending on the insulator thickness due to changes in the oxide interface and electrode microstructure; hence, it would be critical to control the oxide thickness and roughness as well as the electrode microstructure during the deposition process.