The availability of trajectories tracking the geographical locations of people as a function of time offers an opportunity to study human behaviors. In this article, we study rationality from the perspective of user decision on visiting a point of interest (POI) which is represented as a trajectory. However, the analysis of rationality is challenged by a number of issues, for example, how to model a trajectory in terms of complex user decision processes? and how to detect hidden factors that have significant impact on the rational decision making? In this study, we propose Rationality Analysis Model (RAM) to analyze rationality from trajectories in terms of a set of impact factors. In order to automatically identify hidden factors, we propose a method, Collective Hidden Factor Retrieval (CHFR), which can also be generalized to parse multiple trajectories at the same time or parse individual trajectories of different time periods. Extensive experimental study is conducted on three large-scale real-life datasets (i.e., taxi trajectories, user shopping trajectories, and visiting trajectories in a theme park). The results show that the proposed methods are efficient, effective, and scalable. We also deploy a system in a large theme park to conduct a field study. Interesting findings and user feedback of the field study are provided to support other applications in user behavior mining and analysis, such as business intelligence and user management for marketing purposes.