The optimal method of the polymer Materials Informatics (MI) has not been developed because the amorphous nature of the higher-order structure affects these properties. We have now tried to develop the polymer MI's descriptor of the higher-order structure using persistent homology as the topological method. We have experimentally studied the influence of the MD simulation cell size as the higher-order structure of the polymer on its electrical properties important for a soft material sensor or actuator device. The all-atom MD simulation of the polymer has been calculated and the obtained atomic coordinate has been analyzed by the persistent homology. The change in the higher-order structure by different cell size simulations affects the dielectric constant, although these changes are not described by a radial distribution function (RDF). On the other hand, using the 2nd order persistent diagram (PD), it was found that when the cell size is small, the island-shaped distribution become smoother as the cell size increased. There is the same tendency for the condition of change in the monomer ratio, the polymer chain length or temperature. As a result, the persistent homology may express the higher-order structure generated by the MD simulation as a descriptor of the polymer MI.