Abstract In this research, a newly proposed method combining Chemkin with CONVERGE was used to study the transient in-cylinder chemical reaction process in NG-diesel dual fuel engine. The selected mechanism was verified by comparing the results of CONVERGE with experimental data, and then the calibrated model of CONVERGE was used to provide boundary conditions for Chemkin. On this basis, the detailed combustion process was simulated at different natural gas substitution ratio (NGSR). The results show that, the chain branching reaction, long-chain to short-chain reaction, and reactions associated with OH radicals have significant impacts on temperature. It can also be found that the combustion of fuel shows a distinct two-stage reaction process. During the low temperature stage, both the CO and NO emissions are little. While at the high temperature stage, the CO emissions first rapidly increase and then decrease due to the consumption reaction, and the NO emissions also have a quick increase. When the NGSR is reduced, a new path for CO generation occurs at low temperature stage, resulting in minor increase (up to 0.0019 mol fraction) of CO concentration. Meanwhile, the ignition delay is reduced significantly (by 88.5%), but the increase of diesel species does not alter the formation mechanism of emissions. All these provide guidance for improving combustion and emission performance of NG-diesel dual fuel engine.