This study was undertaken to develop a method of numerical performance prediction for application to the development of controlled-auto-ignition (CAI) natural gas engines. By using a combustion model based on analyzed combustion data and introducing this to a commercial one-dimensional gas dynamic simulator, we attempted to establish a means of attaining a highly accurate performance prediction while reducing the calculation load. The combustion model was separately calibrated for two models, namely, the auto-ignition timing of the combustion and the mass fraction burned. As a result, the combustion modeling was able to successfully predict the accuracy of the auto-ignition timing difference at 0.03 degree of crank angle on average, and 0.95 degree in the 2σ region. Furthermore, the functions of the mass fraction burned were expressed using closely correlated in-cylinder parameters. To investigate the application of this numerical performance prediction method, a parametric study to maximize the thermal efficiency of CAI natural gas engines was conducted. Different engine configurations with stroke /bore ratios of 1.0 to 2.5 and intake/exhaust valve diameter ratios of 0.8 to 1.4 were examined, with the maximum net indicated thermal efficiency being 45% for a stroke/bore ratio of about 2.0.and an intake/exhaust valve diameter ratio of 1.0. Using this approach, it is possible to predict the performance by specifying the configuration, while reducing the calculation load involved in a parameter study of CAI engines with a wide range of specifications. Moreover, the measured data can be stored as combustion data for incorporation into the model used for simulation. Also, this simplified experiment-based combustion model could be implemented in the engine electric control unit to ensure the stable running of a CAI natural gas engine.