The influence of the magnetization configuration on Kondo effect in magnetic tunnel junction is investigated. In the parallel configuration, an additional resistance contribution (R*) below 40 K exhibits a logarithmic temperature dependence, indicating the presence of Kondo effect. However, in the anti-parallel configuration, the Kondo-effect-associated spin-flip scattering has a nontrivial contribution to the tunneling current, which compensates the reduction of the current directly caused by Kondo scattering, making R* disappear. These results indicate that suppression and restoration of Kondo effect can be experimentally achieved by altering the magnetization configuration, enhancing our understanding of the role of Kondo effect in spin-dependent transport.