Data stream is a type of data that continue to grow over time. For example, network security data stream will constantly be generated in the field of data security, and encrypted data stream will be generated in the privacy protection scenario. Clustering is a basic task in the analysis of data stream. In addition to the large amount of data and limited computer memory, there are the following challenges in time-decaying data stream clustering: (1) How to quickly process time-varying data stream and how to quickly save vaild data. (2) How to maintain and update clusters and track their evolution in real time. Based on the fact that the existing data stream algorithms do not provide a good strategy to the above problems, this paper proposes a dynamic clustering algorithm named SKDStream. The algorithm divides the entire data space into distinct minimal bound hypercubes, which are maintained and indexed by a newly defined structure, SKDTree, that aggregates and updates clusters in real time without requiring large primary storage. Clusters are composed of dense hypercubes. Experiments on synthetic datasets and real datasets show that the response time of the algorithm is similar to that of existing dataflow algorithms, but the quality of the generated clusters is relatively stable over time. Furthermore, the SKDStream algorithm is able to track the evolution of the number of clusters, centers, and density in real time, and compared to D-stream, SKDStream is efficient and effective in clustering.