Cluster-based protocols are best for applications that require reliability and a continuous functioning environment with a sustainable lifetime of WSN. The dynamic nature of the sensor node makes energy conservation a challenging issue. Sensor node scheduled based on sensing error for energy conservation compromise the accuracy of prediction. The high data accuracy achieved using a single duty cycle controller at each node with compromised throughput and increased routing overhead. Duty Cycle Controller managing a more number of control messages at the network level leads to control packet interference with data packet transmission, increasing packet drop and minimizing throughput. Also, the single-duty cycle controller at the network level leads to increased control overhead. The proposed multilevel cluster-based approach focuses on the appropriate cluster design, selection of cluster head, and sensor nodes scheduling based on sensing error. The proposed method applies a multi-duty cycle controller at each cluster level, and control messages handled are related to nodes in a cluster. Thus has less interference and packet drop leading to maximum throughput than existing methods. The simulation results demonstrated that the proposed method with sensor nodes scheduled at individual cluster levels using a multi-duty cycle controller exhibited improved network lifetime, throughput, and reduced energy consumption compared with the state-of-the-art techniques.