The incorporation processes of Mn2+ and Co2+ into the framework of aluminophosphate molecular sieve AlPO4-5, at the onset of crystallization, were investigated by in situ synchrotron X-ray absorption spectroscopy (XAS) and density functional theory (DFT) computation. The results indicated that the syntheses of MnAPO-5 and CoAPO-5 were different in the incorporation mechanism of metal ions. For the synthesis of CoAPO-5, Co2+ transferred from an octahedral into tetrahedral structure with crystal formation, while, for MnAPO-5, the Mn2+ transition to the tetrahedral structure was much more difficult and it occurred after the appearance of long-range ordered microporous structure. The DFT computations of model intermediates involved in the synthesis process suggested that much higher transformation energy of [Mn(OP(OH)(3))(4)](2+) than that of [Co(OP(OH)(3))(4)](2+) was responsible for the diversity of the incorporation behaviors.