Cyclic variation is a serious problem for two stroke engines at low load conditions. Misfire and partially burned cycles occur and the unburned hydrocarbons in the exhaust are extremely high. The occurrence of variations seems random. However, there are some rules behind this seemingly chaotic process. The combustion of one cycle is affected by the concentration of residual gas in the cylinder, which is the result of the scavenging process of pre-cycles. An engine cycle model has been developed in a previous paper which can simulate the cyclically varied process and generate chaotic or multi-cycle periodic engine performance. In this paper, the engine cycle model was refined, and the calculated results of misfire rates and the HC and the CO emissions were compared with measured data.The residual gas concentration in the cylinder prior to ignition was used as the criterion to determine a successful ignition in the previous model. In this paper, an energy balance in the flame kernel at ignition point was used to replace the old criterion. Results of simulation showed that these two criteria are equivalent at some engine conditions. Furthermore, a flexible scavenging model was used in this paper which can switch between the perfect mixing model and the perfect displacement model or any combination of these two models.Results of calculations were compared with the measured data at low load engine conditions. The misfire rate and the short circuit ratio agree well with experimental data in trend. The trends of variation for the HC and the CO emissions while equivalence ratio was varied are consistent with the measured data. However, the magnitudes of calculated emissions are about 30% higher than the measured data.