This study aimed to detect the spatial distribution and high-risk clusters of female breast cancer mortality for the years 2011 to 2013 in Shandong Province, China. The urban-rural difference in the spatial distribution and clusters of disease mortality were also examined. Breast cancer mortality data were obtained from the Shandong Death Registration System (SDRS) during 2011 to 2013 and were adjusted for the underreporting rate. The purely spatial scan Statistics method was performed using Discrete Poisson model. Seven significant spatial clusters for high mortality of female breast cancer were detected in Shandong Province at the county level; these clusters were mainly located in the eastern, southern, southwestern, central and northern regions. The spatial distributions differed significantly between urban and rural populations. Population ageing influenced the distribution of breast cancer clusters for the urban eastern residents. This study provided evidence for the presence of clusters of breast cancer mortality in Shandong, China and found urban-rural difference in the clusters, which is helpful for developing effective strategies to control breast cancer in different areas.