This paper proposes a novel Hierarchical Clustering algorithm based on the Micro-Cluster strategy, called HCMC algorithm. In order to alleviate the influence caused by the noise data on the quality of clustering, the concept of density-based is applied to data partition and filtration of noise data. The HCMC algorithm consists of two phases. The first phase aims to partition several micro-clusters and then filter out noise data by using the density-based method for keeping the main data of clusters. The second phase uses single-linkage agglomerative algorithm to explore of arbitrary shapes. With the partitioning phase, the process of agglomeration is efficient. The experiment demonstrates that HCMC algorithm is capable of reducing the impact on clustering caused by noise data and keeping a fair quality of clustering as well. In the meantime, HCMC algorithm also proves to be superior to other clustering algorithms among the same categories as far as the complicated time calculation is concerned.