Controlled synthesis of 3D polymer networks presents a significant challenge because of the complexity of the polymerization reaction in solution. In this study, a polymerization system that facilitates the prediction of a polymer network structure via percolation simulations is realized. The most significant difference between general percolation simulations and experimental polymerization systems is the mobility of the molecules during the reaction. A crystal component-linking method that connects the precisely arranged monomer as a supramolecular crystalline state to imitate the simple percolation theory is adopted. The percolation simulation based on the crystal structure of the arranged monomers is used to accurately calculate the gelation point, gel fraction, degree of swelling, and atomic formula, which correspond with the experimental results. This suggests that the network structures polymerized via the crystal component-linking method can be predicted precisely by a simple percolation simulation. Further, the percolation simulation predicts the structures of the loop, branched polymer, and crosslinking point, which are difficult to measure experimentally. The polymerization of precisely-arranged immobilized monomers in supramolecular structures is promising in synthesizing precisely controlled polymer networks.