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Although micro-mesoporous composite molecular sieves have received significant attention due to their desirable properties, they still lack systematic studies on their crystallization process to achieve controllable synthesis of composite molecular sieves. In this study, a series of Y/SBA-15 micro-mesoporous composite molecular sieves with different porous structures were synthesized by tuning nucleation temperature, based on epitaxial growth on the outer surface of the Y-type crystal particle. All composite molecular sieves were characterized by X-ray diffraction (XRD), scanning electron microscope (SEM), and transmission electron microscope (TEM). Moreover, the effect of nucleation temperature on the structure of composite molecular sieves was investigated, while the crystallization mechanism was also explored. Furthermore, the performance of the molecular sieves on isomerization of n-pentane was investigated, the results suggested that the isomerization selectivity was positively correlated with regularity degree of the mesoporous porous structure, where the highest isomerization reached 95.81%. This work suggests that nucleation temperature plays a key role in structures of micro-mesoporous composite molecular sieves, providing a solid basis for the further development of functional composite molecular sieves.