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Throughput maximization is a key challenge for wireless applications in cognitive Vehicular Ad-hoc Networks (C-VANETs). As a potential solution, cooperative communications, which may increase link capacity by exploiting spatial diversity, has attracted a lot of attention in recent years. However, if link scheduling is considered, this transmission mode may perform worse than direct transmission in terms of end-to-end throughput. In this paper, we propose a cooperative communication aware link scheduling scheme and investigate the throughput maximization problem in C-VANETs. Regarding the features of cooperative communications and the availability of licensed spectrum, we extend the links into cooperative links/general links, define extended link-band pairs, and form a 3-dimensional (3-D) cooperative conflict graph to characterize the conflict relationship among those pairs. Given all cooperative independent sets in this graph, we mathematically formulate an end-to-end throughput maximization problem and near-optimally solve it by linear programming. Due to the NP-completeness of finding all independent sets, we also develop a heuristic pruning algorithm for cooperative communication aware link scheduling. Our simulation results show that the proposed scheme is effective in increasing end-to-end throughput for the session in C-VANETs.