Wireless caching enables popular files to be stored at the base stations (BSs) in advance, which has been considered as an efficient way to reduce the service delay and alleviate heavy burdens on the backhaul links. In this paper, we study the BS clustering scheme for the cooperative wireless caching networks (CWCNs) with heterogeneous file preference among users and BSs, and propose the minimum cost (MC) based clustering scheme. We first introduce the weight-based cost function, which characterizes the trade-off between service delay and transmission cost, and then formulate the clustering as the optimization problem. Furthermore, two clustering algorithms are developed to solve the optimization problem. The results show that the proposed scheme can achieve lower cost compared with random clustering scheme.