BackgroundAlthough the incidence of tuberculosis (TB) in most parts of China are well under control now, in less developed areas such as Qinghai, TB still remains a major public health problem. This study aims to reveal the spatio-temporal patterns of TB in the Qinghai province, which could be helpful in the planning and implementing key preventative measures.MethodsWe extracted data of reported TB cases in the Qinghai province from the China Information System for Disease Control and Prevention (CISDCP) during January 2009 to December 2016. The Kulldorff’s retrospective space-time scan statistics, calculated by using the discrete Poisson probability model, was used to identify the temporal, spatial, and spatio-temporal clusters of TB at the county level in Qinghai.ResultsA total of 48,274 TB cases were reported from 2009 to 2016 in Qinghai. Results of the Kulldorff’s scan revealed that the TB cases in Qinghai were significantly clustered in spatial, temporal, and spatio-temporal distribution. The most likely spatio-temporal cluster (LLR = 2547.64, RR = 4.21, P < 0.001) was mainly concentrated in the southwest of Qinghai, covering seven counties and clustered in the time frame from September 2014 to December 2016.ConclusionThis study identified eight significant space-time clusters of TB in Qinghai from 2009 to 2016, which could be helpful in prioritizing resource assignment in high-risk areas for TB control and elimination in the future.Electronic supplementary materialThe online version of this article (doi:10.1186/s12879-017-2643-y) contains supplementary material, which is available to authorized users.