This work reports a novel method to selectively synthesize framework isomer MOF crystals. Al-MIL-100 and Al-MIL-96 are framework isomers and could be obtained purposefully by adding an inducing agent using a microwave irradiation method. The inducing agent has an occupying effect by a PO4 tetrahedron group, which favors the formation of basic building units of Al-MIL-100. Spontaneously, zeolite AlPO4 or SAPO-34 was employed as an inducing agent for rapid and controllable synthesis of single phase Al-MIL-100. The results show that the gradual releasing of phosphate from the solid surface during the early stage of synthesis plays a crucial role in the occupying action. Subsequently, a possible growth mechanism of Al-MIL-100 is proposed. Finally, the resulting Al-MIL-100 exhibits a nice stability and a remarkable selective adsorption ability for N-heterocyclic molecules from fuels.