Process of a silica cluster on a polyimide surface was simulated by atomistic calculations combining the semi-empirical molecular orbital method and algorithms that can find the optimal path of a chemical bonding process. Specifically, we estimated the activation and sorption energies in the process. From the simulations, we found that chemical bonding occurs between a silica cluster and the polyimide substrate surface. In the adsorption processes, those reactions between the silica cluster and the polyimide surface which involve Si-O bonding between the cluster and the polyimide are the most probable.