One of the major reason for performance degradation in Wireless sensor network is the overhead due to control packet and packet delivery degradation. Clustering in cross layer network operation is an efficient way manage control packet overhead and which ultimately improve the lifetime of a network. All these overheads are crucial in a scalable networks. But the clustering always suffer from the cluster head failure which need to be solved effectively in a large network. As the focus is to improve the average lifetime of sensor network the cluster head is selected based on the battery life of nodes. The cross-layer operation model optimize the overheads in multiple layer and ultimately the use of clustering will reduce the major overheads identified and their by the energy consumption and throughput of wireless sensor network is improved. The proposed model operates on two layers of network ie., Network Layer and Transport Layer and Clustering is applied in the network layer . The simulation result shows that the integration of two layers reduces the energy consumption and increases the throughput of the wireless sensor networks.