Smart card systems for public transport have been rapidly growing in the world. When a smart card holder goes through a ticket gate, the gate passing time of the card holder is recorded very short time interval such as every one minute. When those data are stored, the historical record of the smart card usage can provide an accurate data set for analyzing the movement of users of public transport. Smart card data are attractive for railway companies when they discuss train operation designs and pricing strategies. It becomes possible to evaluate the detailed effects of transport policies and operations on user's behavior. The smart card data could show how the introduction of a measure of railway changes user's behavior. The aims of this paper are to propose the methodologies for estimating the behavior of railway passengers using the smart card data, and to analyze the effects of new train operations.