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Accurate and timely estimations of large-scale population distributions are a valuable input for social geography and economic research and for policy-making. The most popular large-scale method to calculate such estimations uses mobile phone data. We propose a novel method, firstly based upon using a kernel density estimation (KDE) to estimate dynamic mobile phone users’ distributions at a two-hourly scale temporal resolution. Secondly, a convolutional long short-term memory (ConvLSTM) model was used in our study to predict mobile phone users’ spatial and temporal distributions for the first time at such a fine-grained temporal resolution. The evaluation results show that the predicted people’s mobility derived from the mobile phone users’ density correlates much better with the actual density, both temporally and spatially, as compared to traditional methods such as time-series prediction, autoregressive moving average model (ARMA), and LSTM.