Interchange provides more flexibility in route choice, a key travel behaviour in urban rail transit, but its influence is usually simplified. This paper investigates how interchange affects route choice with passenger perception considered. At single-interchange level, perceived interchange time was proposed and modelled under three resolutions to capture passenger perception and its sensitivity. At route level, the influence of interchange was modeled by first comparing eight quantifications of interchange. Mixed logit models with the best interchange proxy were further developed to address the correlation among alternative routes and reveal the potential taste variations among passengers. Results based on Shanghai Metro data showed perceived interchange time, including passenger perception and interchange environment, better represents the influence of interchange in route choice, meanwhile the weights of interchanges on one route rise sequentially and non-linearly. The results can improve route choice prediction in demand modelling and route recommendation in advanced traveller information systems.