The energy of the node in the Wireless Sensor Networks (WSNs) is scare and causes the variation in the lifetime of the network. Also, the throughput and delay of the network depend on how long the network sustains i.e. energy consumption. One way to increase the sustainability of network is the introduction of heterogeneous nodes regarding energy, and the other is to synchronize the local clock of the node with the global clock of the network. In this context, the paper proposes Node Heterogeneity aware Energy Efficient Synchronization Algorithm (NHES). It works on the formation of cluster-based spanning tree (SPT). In the initial stage of the algorithm, the nodes are grouped into the cluster and form the tree. The nodes in the cluster and cluster heads in the network are synchronized with the notion of the global time scale of the network. Also, clock skews may cause the errors and be one of the sources of delay and energy consumption. To minimize the energy consumptions and delay, NHES synchronizes the time slots using TDMA based MAC protocol. The results show that level by level synchronization used in NHES is energy efficient and has less delay as compared to the state-of-the-art solutions.