A novel synthesis route for a MCM-41 structure with Y zeolite seeds colloidal has been developed. The route is different from conversational method of highly ordered MCM-41 assembled from Y zeolite seed colloidal. The material was characterized by various techniques. The results indicate that the material has well-ordered hexagonal structure, with a thicker wall than that of the sample synthesized by a direct hydrothermal route (N-MCM-41). SEM images show a very uniform net-like morphology, which is different from the loose appearance of N-MCM-41. Furthermore, it has a stronger acid strength and a higher hydrothermal stability. The sample was used as the support of a Pd-Pt catalyst for the polyaromatics hydrogenation. It was demonstrated that the introduction of building units of Y zeolite enhances the activity of polyaromatics hydrogenation. It can be concluded that the pore structure and acidity of support is a key factor for the design of a sulfur tolerant noble metal catalyst for aromatics saturation of diesel.