A new two conserved scalar regenerative multiple zones model (REMUZ) is proposed in the present work. The model simulates the in-cylinder combustion characteristics of novel engines based on the premixed charge stirred chemical reactor (PCCI, HCCI). In this two conserved scalar approach, the mixture fraction (X) and initial exhaust fraction (F) are used to determine the state of in-cylinder homogeneously stirred chemical reactor reactive system, which is advancement over the established single conserved scalar approach of using fuel and oxidizer as separate entities. The reactive system in two conserved scalar regenerative model was divided into multiple zones-each representing premixed homogeneous charge stirred reactor with uniquely determined distribution of initial exhaust gases at a defined mixture fraction, mixed, regenerated and determined uniquely at each combustion step. A description of the mathematical model and the methodology of its solution for developing REMUZ algorithm are presented. The methodology for creating and consuming each zone is proposed. Initially, the consistency of the new model is validated for the use of different heat transfer correlations. Next, study to establish the optimum number of zones needed to perform parametric study was done. Finally, a parametric study is performed to investigate the sensitivity of the key combustion characteristics to different engine parameters was undertaken and presented.