The Hosoya index m(G) and the Merrifield–Simmons index i(G) of a graph G are the number of matchings and the number of independent sets in G. In this paper, we establish exact formulas for the expected value of the Hosoya index and Merrifield–Simmons index of the random cyclooctylene chains, which are graphs of a chemical chain consisting of n octagons, each of which is connected to the end of the previous octagon by an edge. In addition, we obtain the expected values and the average values of the two indexes through the relevant chemical diagrams and a series of accurate formulas with respect to the set of all cyclooctylene chains with n octagons.