Human mobility data accumulated from Point-of-Interest (POI) check-ins provides great opportunity for user behavior understanding. However, data quality issues (e.g., geolocation information missing, unreal check-ins, data sparsity) in real-life mobility data limit the effectiveness of existing POIoriented studies, e.g., POI recommendation and location prediction, when applied to real applications. To this end, in this paper, we develop a model, named Bi-STDDP, which can integrate bi-directional spatio-temporal dependence and users’ dynamic preferences, to identify the missing POI check-in where a user has visited at a specific time. Specifically, we first utilize bi-directional global spatial and local temporal information of POIs to capture the complex dependence relationships. Then, target temporal pattern in combination with user and POI information are fed into a multi-layer network to capture users’ dynamic preferences. Moreover, the dynamic preferences are transformed into the same space as the dependence relationships to form the final model. Finally, the proposed model is evaluated on three large-scale real-world datasets and the results demonstrate significant improvements of our model compared with state-of-the-art methods. Also, it is worth noting that the proposed model can be naturally extended to address POI recommendation and location prediction tasks with competitive performances.