The thermodynamic picture describing the formation mechanism of bicontinuous concentric lamellar (bcl) nanostructured silica particles, bcl silica, was investigated thoroughly. A series of classical kinetics of bcl silica by varying the synthesis time were employed to observe the morphological evolution of bcl silica. The formation mechanism of bcl silica is proposed as the hydrolysis and condensation reactions in the reverse micelle, followed by the phase segregation process. The images of the whole part and the cross-section of bcl silica reveal that bcl silica can be obtained just 30 min after the synthesis starts. The particle morphology evolves from bicontinuous lamellar (bl) morphology, with the absence of the dense part in the center of the particle, to bicontinuous concentric lamellar (bcl) morphology. The theoretical part of this study is focused on the phase segregation process of the mixture. This process is divided thermodynamically into several reversible processes based on the reduced Helmholtz free energy state function. The type of the lamellar orientation (i.e., parallel or perpendicular orientation) changed as the stacked lamellae changed in thickness and was followed by the decrease in the free energy. It was merely shown that the segregation of the thin slab of the lamellar polysiloxane stack favors the perpendicular orientation. In contrast, the thick slab of the lamellar polysiloxane stack yields a complex lamellar structure consisting of perpendicular and parallel orientations. A lamellar polymer confined between two planar substrates can experience a topological transformation into a sphere due to an unfavorable environment, i.e., high surface tension. After the topological transformation, lamellae with a perpendicular orientation form bicontinuous lamellae, whereas the complex lamellar structure transforms into a bicontinuous concentric lamellar morphology.