During these years, the 3D node coverage of heterogeneous wireless sensor networks that are closer to the actual application environment has become a strong focus of research. However, the direct application of traditional two-dimensional planar coverage methods to three-dimensional space suffers from high application complexity, a low coverage rate, and a short life cycle. Most methods ignore the network life cycle when considering coverage. The network coverage and life cycle determine the quality of service (QoS) in heterogeneous wireless sensor networks. Thus, energy-efficient coverage enhancement is a significantly pivotal and challenging task. To solve the above task, an energy-efficient coverage enhancement method, VKECE-3D, based on 3D-Voronoi partitioning and the K-means algorithm is proposed. The quantity of active nodes is kept to a minimum while guaranteeing coverage. Firstly, based on node deployment at random, the nodes are deployed twice using a highly destructive polynomial mutation strategy to improve the uniformity of the nodes. Secondly, the optimal perceptual radius is calculated using the K-means algorithm and 3D-Voronoi partitioning to enhance the network coverage quality. Finally, a multi-hop communication and polling working mechanism are proposed to lower the nodes’ energy consumption and lengthen the network’s lifetime. Its simulation findings demonstrate that compared to other energy-efficient coverage enhancement solutions, VKECE-3D improves network coverage and greatly lengthens the network’s lifetime.