Service disruptions of rail transit systems have become more frequent in the past decade in urban cities, due to various reasons, such as power failures, signal errors, and so on. Smart transit cards provide detailed tapping records of commuters, which enable us to infer their trajectories under both normal and disruptive circumstances. In this article, we study and predict the impact of disruptions on commuters and further evaluate the vulnerability of the rail system. Specifically, we define two metrics, stay ratio and travel delay, to quantify the impact, and we derive the predictor of each metric based on the inferred alternative route choices of commuters under disruptive circumstances. We demonstrate that the alternative route choices contribute to more similar feature distribution among different disruptions, which is crucial to tackling the main challenge of abnormal data scarcity and is beneficial for obtaining more reliable predictors for future disruptions. We evaluate our approach with a real-world transit card dataset. The result demonstrates the effectiveness of our method. Based on the predictors, we further analyse the vulnerability of the rail system. An evaluation with cross validation from taxi GPS trajectory data indicates its efficacy in discovering vulnerable rail stations as well as Origin-Destination pairs.