Nucleation kinetics of the precipitation for MnAl6 and MnAl12 in the aluminum alloy AA3003 alloy have been investigated experimentally and theoretically. The results show that cold rolling enhances the rate of precipitation and this effect increases as the annealing temperature decreases. Micro-segregation of the solute atom Mn at the dislocation network during cold deformation is found to have a significant effect on the nucleation kinetics of the precipitation of MnAl6 and MnAl12 in AA3003 in addition to the effect of dislocations, which increase the nucleation site density and reduce the nucleation barrier. A model to predict the start times of the precipitation during isothermal holding is constructed by considering the effects of dislocations and recovery as well as micro-segregation of Mn on the nucleation kinetics of precipitates. The predictions of the model are in good agreement with the experiment data.