This paper presents a research work on intelligent two-stage modelling system to estimate a hydrogen internal combustion engine performances including: engine torque and oxides of nitrogen emissions. In the created models, the ignition timing is chosen as a local input, while the engine speed, throttle position, injection duration, injection end angle and lambda are chosen as global inputs. While previous papers [1-4] included tuning procedures and hydrogen engine performances, intelligent emissions prediction of hydrogen car, and two-stage modelling of torque, this paper carries on from those observations to develop a completed two-stage modelling system of the converted hydrogen engine. More details on individual two-stage models are provided based on data recorded during the fine tuning process on dynamometer. This work is a step towards establishing intelligent two-stage modelling of hydrogen powered car via application of response surface methodology with hydrogen engine in the loop simulation and testing. Copyright (C) 2011, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved.