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Understanding population distribution has excellent applications for planning and provision of municipal services. This study aims to explore the space-time structure of population distribution with area-level mobile phone data. We discuss a kind of Bayesian hierarchical models, fitted by Markov chain Monte Carlo simulation, that combines the overall spatial pattern and temporal trends as well as the departures from these stable components. We carry out an empirical study in Shenzhen, China, using the area-level mobile phone users in 24 hours. The results indicate that the estimation of the overall spatial pattern is not deteriorated when using a sophisticated spatio-temporal model. The temporal trend exhibits a reasonable fluctuation during the study period. Then we apply two rules to detect areas showing unstable trends of population fluctuation based on the posterior probabilities of the space-time interactions. We also include the population statistics and indices for mixed-use to explore the spatial pattern of population fluctuation. Our findings confirm that the Bayesian spatio-temporal model can enhance the understanding of the space-time variability of population distribution using mobile phone data. Further research should examine the spatial nonstationary effects of explanatory factors on mobile phone-based population fluctuation. [ABSTRACT FROM AUTHOR]