•A multiscale radial basis function (MSRBF) network is proposed.MSRBF network can predict irregular subway passenger flow under special events.•MSRBF network can pinpoint vulnerable subway stations for crowd control measures.•MSRBF network significantly outperforms traditional prediction methods. Reliable and accurate short-term subway passenger flow prediction is important for passengers, transit operators, and public agencies. Traditional studies focus on regular demand forecasting and have inherent disadvantages in predicting passenger flows under special events scenarios. These special events may have a disruptive impact on public transportation systems, and should thus be given more attention for proactive management and timely information dissemination. This study proposes a novel multiscale radial basis function (MSRBF) network for forecasting the irregular fluctuation of subway passenger flows. This model is simplified using a matching pursuit orthogonal least squares algorithm through the selection of significant model terms to produce a parsimonious MSRBF model. Combined with transit smart card data, this approach not only exhibits superior predictive performance over prevailing computational intelligence methods for non-regular demand forecasting at least 30min prior, but also leverages network knowledge to enhance prediction capability and pinpoint vulnerable subway stations for crowd control measures. Three empirical studies with special events in Beijing demonstrate that the proposed algorithm can effectively predict the emergence of passenger flow bursts.