The present invention relates to a method of preparing a microporous crystalline molecular sieve having mesoporous skeleton, comprising following steps: (a) adding a meso-SDA (meso-Structure Directing Agent) into a gel composition of synthesizing molecular sieve, (b) subjecting the mixture obtained in the above step (a) to crystallization by a hydrothermal reaction, a microwave reaction, a dry-gel synthesis, etc., and (c) removing selectively organic materials from the resulted material obtained in the above step (b) by a calcination or a chemical treatment. Molecular sieve having mesoporous skeleton synthesized by the present invention exhibits, as compared with conventional zeolite, a good molecule diffusion ability and a greatly improved catalytic activity.