The human origin-destination (OD) flow prediction is of great significance for urban safety control, stampede prevention, disease transmission control, urban planning, and many other aspects. Most of the existing methods generally divide the urban area into grids and use vehicle GPS trajectories and metrocard check-in data, combined with machine learning or deep learning models to predict human OD flow. However, these kinds of methods are challenging to capture fine-grained human mobility patterns. Moreover, these methods usually deviate from the actual human OD transfer patterns on a citywide scale due to the particularity of different datasets. To this end, in this paper, we use large-scale mobile phone signal data to achieve human OD flow prediction between the coverage of varying signal base stations. Many signal base stations are distributed in urban geographical space, collecting all the mobile phone user’s location information to obtain large-scale fine-grained unbiased human OD flow data. Due to the lack of natural topology structure between base stations, this paper adopts a TGCN model combined with a graph fusion module to pretrain the dynamic population distribution prediction task. The parameters of the graph fusion module are employed to capture the different semantic information in the proposed hybrid machine learning method and finally achieve citywide human OD flow prediction. Extensive experiments on the real-world signal datasets in Changchun, China, demonstrate the effectiveness of our model.