A few aluminophosphate (AlPO) molecular sieves are synthesized hydrothermally under microwave irradiation and conventional electric heating. Less stable AlPO molecular sieves especially with large pore can be obtained preferentially in a short crystallization time because the inter-conversion of less stable phase into a more stable one is prohibited in short reaction time. The VFI transforms into AFI, and finally into APC, with the increase of reaction time since the relative stability is VFI < AFI < APC under the chosen reaction conditions. The relative stability can be explained with the pore size or by the framework density of each structure. Due to the rapid crystallization involved in the microwave method and instability of porous materials with large pore, these porous materials can be selectively synthesized by microwave irradiation. The synthesis of extra-large-pore VPI-5 using triethylamine is also reported for the first time, and the synthesized VPI-5 is very stable that can be dried at 100 degrees C at atmospheric pressure without the phase-transformation into AIPO-8.