The magnetic ordering and relative structural stability (phase diagram) of La2/3Sr1/3MnO3/SrTiO3 (LSMO/STO) (001) interfaces are considered by performing generalized gradient approximation plus on‐site Coulomb correction calculations. A potential antiferromagnetic alignment between the interface layer and bulk is conjectured for the b‐type LSMO/STO (001) interface where the atomic‐layer stacking near interface is $\cdots $LaOMnO2LaOMnO2SrOMnO2SrOTiO2$\cdots $ (SrO termination). This is in qualitative agreement with the fact that suppression of ferromagnetism at the SrO‐terminated (001) interface is found at some experiments. The small magnetic exchange energies, for the SrO‐terminated LSMO/STO (001) interfaces, suggest that Mn spins at the interface are likely to reverse as the temperature changes. Hence, possible magnetic reconstructions will be expected to occur at the SrO‐terminated (001) interfaces when temperature increases. Under thermodynamic equilibrium, the calculated phase diagrams show that, with the exception of the c‐type (001) interface where the atomic‐layer stacking near interface is $\cdots $La2/3Sr1/3OMnO2SrOTiO2$\cdots $ (SrO termination), all other considered LSMO/STO (001) interfaces may be stabilized in the proper conditions. The spin‐resolved density of states shows that high spin‐transport behaviors could be achieved at the ferromagnetic TiO2‐terminated (001) interfaces. The results of the calculations can compare favorably with the experimental results for the LSMO/STO (001) junctions.