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This study presents a non-linear longitudinal dynamic model of high speed trains by considering the rolling stock, train formations, rolling resistance, track environment, etc., and longitudinal controller design for Automatic Train Operation (ATO) as well. For a controller design, a novel hybrid model reference based adaptive super twisting sliding mode control scheme is proposed. The control law comprises a non-linear model reference adaptive control (MRAC) and an adaptive second order sliding mode control (SMC) in order to make the control signal continuous and to alleviate the chattering phenomenon. The adaptive gains of the proposed control law are derived based on Lyapunov approach that ensures global stability with exact tracking in finite time. A linear stable reference model is developed with the ideal train-track parameters to generate the reference trajectory. The effectiveness of the presented concept is demonstrated by introducing load variation, model uncertainties and external disturbances in the non-linear model of the train and its performance is compared with the non-linear MRAC and the second order sliding mode controller. [ABSTRACT FROM AUTHOR]