In modern methods of synthesis of nanostructured materials based on mesoporous silica matrices (MCM-41, SBA-15), it is not possible to simultaneously fine adjust both the pore diameter and the thickness of the separating walls. This article presents the results of work on the creation of composites based on mesoporous silica matrices MCM-41 and SBA-15, reinforced with metallic Fe nanoparticles (Fe NPs). The article considers a new way of ultrafine regulation of the pore radius and separating wall thickness mesoporous silica SBA-15. In this work, we studied the changes in their structural and magnetic characteristics by directionally adjusting the geometric parameters of the porous structure of the initial matrices. The following methods are applied to adjust the silica pore parameters: hydrothermal treatment and templating using a micellar expander. The technique is based on building up aluminum-oxygen nanolayers on the pore walls using gas-phase atomic layer deposition technique (ALD). Studying room-temperature magnetization of Fe NPs obtained during the synthesis in a matrix of mesoporous silica MCM-41 (pore size of 3–5 nm) allowed us to establish superparamagnetic properties of such magnetic materials, which allows to use them in medicine for targeted drug delivery. Fe NPs in the mesoporous silica SBA-15 matrix with a pore size of 3–6 nm also exhibit superparamagnetic properties, and these composites showed a coercive force increase with an increase in the original matrix pore size.