In this paper, based on experiment result in a hydrogen fueled engine, pre-ignition and transforming process from pre-ignition to backfire of the hydrogen fueled engine was analyzed. Moreover, mechanism of pre-ignition and backfire of hydrogen fueled engines was studied by analyzing chain reaction. The analysis shows that the temperature, pressure and rate of pressure rise have great influence on pre-ignition and backfire. And based on thermodynamic relations of heat release rate, both pre-ignition and backfire were also analyzed. Finally, optimization control model which has multi-variables, multi-objectives and multi-constraints was established. And the simulation was carried out through the genetic algorithm. Results have shown that the excess air ratio and ignition advance angle can be adjusted by weighted coefficients to optimize the power output and restrict the abnormal combustion. Thus, a useful method is shown to resolve the contradictions between restricting the abnormal combustion and improving hydrogen fueled engine's power output. Copyright (C) 2011, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved.