Several cobalt aluminophosphate (CoAPO) molecular sieves are synthesized hydrothermally under microwave irradiation and conventional electric heating. Relatively unstable CoAPO molecular sieves with large pore can be obtained preferentially with microwave synthesis due to the rapid crystallization involved in the microwave method. For example, the VFI (composed of 18 membered rings; 18 MR) and AFI molecular sieves (12 MR), rather than AFI (12 MR) and AEI (8 MR) molecular sieves, respectively, can be selectively produced under the microwave irradiation. On the contrary, from the same reactant gel, more stable CoAPO molecular sieves with relatively small pore are obtained by conventional hydrothermal synthesis for long crystallization time. The AFI and VFI are transformed into AEI and AFI, respectively, with the increase of reaction time because the relative stability of former CoAPOs is less than that of latter CoAPOs under the reaction conditions adopted in this study. The present results suggest that the pore size is a more important to explain the relative stability of CoAPO molecular sieves than the framework density.