Core−shell molecular sieves exhibit excellent performance in many catalytic processes due to their adjustable pore distribution and surface structure. This work developed a silicon coating method for molecular sieves and explored the synthesis method of Y/amorphous-silica composite materials. The effects of ultrasound treatment, silicon source addition amount, and template properties on the amorphous silica structure and properties were determined through comparative experiments. The optimal preparation conditions were obtained, achieving adjustable thickness of the molecular sieve shell. Subsequently, based on the optimal preparation conditions of Y/amorphous silica composite materials, a ZSM-5/silicalite-1 composite molecular sieve with core−shell structure was successfully synthesized, and the structural characteristics of the synthesized core−shell molecular sieve were comprehensively analyzed. The amorphous silica core−shell composite materials prepared in this work achieved directional control of shell thickness and pore structure, providing a promising approach for the preparation of core−shell structures.