Pilot ignited natural gas diesel engine (PINGDE) was demonstrated to achieve low NOx emission, high fuel economy and low fuel cost. Despite of that, PINGDE is still confronted with problems such as high mechanical and thermal stress under heavy load, high CO and THC emission under small load and a trade-off relationship between NOx emission and fuel efficiency for whole operating points.In this study, tests were conducted to explore how three main variables including pilot injection timing, pilot diesel substitution rate and two kinds of pilot injection strategies influence the performance and emission of the modified WP10 engine. Two pilot injection strategies including pilot diesel injected once and twice were proposed and potential of promoting fuel economy and saving fuel cost was demonstrated. Moreover, a numerical engine model is established to optimize engine performance and emission with the help of MBC toolkit through limited experiments.Results show that, dual pilot injection strategy achieved better NOx and methane emission and 2 percent fuel efficiency rise and 5 percent fuel cost saving rate rise under small load. Model based calibration achieved wider high fuel efficiency area and higher fuel cost saving rate than manual calibration results while ESC NOx emission is set to below 5 g/kwh.