Point-of-Interest (POI) recommendation, an important research hotspot in the field of urban computing, plays a crucial role in urban construction. While understanding the process of users’ travel decisions and exploring the causality of POI choosing is not easy due to the complex and diverse influencing factors in urban travel scenarios. Moreover, the spurious explanations caused by severe data sparsity, i.e., misrepresenting universal relevance as causality, may also hinder us from understanding users’ travel decisions. To this end, in this article, we propose a factor-level causal explanation generation framework based on counterfactual data augmentation for user travel decisions, named Factor-level Causal Explanation for User Travel Decisions (FCE-UTD), which can distinguish between true and false causal factors and generate true causal explanations. Specifically, we first assume that a user decision is composed of a set of several different factors. Then, by preserving the user decision structure with a joint counterfactual contrastive learning paradigm, we learn the representation of factors and detect the relevant factors. Next, we further identify true causal factors by constructing counterfactual decisions with a counterfactual representation generator, in particular, it can not only augment the dataset and mitigate the sparsity but also contribute to clarifying the causal factors from other false causal factors that may cause spurious explanations. Besides, a causal dependency learner is proposed to identify causal factors for each decision by learning causal dependency scores. Extensive experiments conducted on three real-world datasets demonstrate the superiority of our approach in terms of check-in rate, fidelity, and downstream tasks under different behavior scenarios. The extra case studies also demonstrate the ability of FCE-UTD to generate causal explanations in POI choosing.