Non-conventional crystallization techniques have been developed in recent years. Non-conventional crystallization techniques use primary structural elements (for example, clusters) rather than atoms and molecules. Modern nanomaterial science is going through great changes as an entirely new approach of non-conventional growth mechanisms is emerging due to cluster coupling, catalyzing interest in cluster physics. The formation of fractal and percolation clusters has increased. We carried out step-by-step modeling and an experimental study of the formation of fractal and percolation clusters based on tin dioxide and silicon dioxide and formed by sol–gel technology. In this paper, the growth of fractal aggregates (clusters) from sol particles SnO2 and SiO2 based on the modified models of diffusion-limited and cluster–cluster aggregation is discussed. A percolation model using simulated fractal clusters of SnO2 and SiO2 particles is proposed. Experimental data on the sol–gel percolation structure of porous nanocomposites are presented. The modeling of SnO2 and SiO2 particles, which also consist of clusters (the next step in the hierarchy), is shown. We propose a generalized hierarchical three-dimensional percolation cluster model that allows calculating the surface area, knowing the experimental sizes of macropores and taking into account the micro- and mesopores (sizes less than a few nanometers).