Low Temperature Combustion (LTC) is known to be feasible only in lower load ranges so in real world application of LTC, engine operation mode should frequently change back and forth between LTC mode in lower loads and conventional mode in higher loads. In this research, effect of injection strategy on smoothness and emissions during mode transition in a single cylinder heavy duty diesel engine is studied. The Exhaust Gas Recirculation (EGR) line was controlled by a servo-valve capable of opening or closing the EGR loop within only one engine cycle. Ten cycles after the EGR valve closure were taken as the transition period during which injection timing and quantity were shifted in various ways (i.e. injection strategies) and the effect on Indicated Mean Effective Pressure (IMEP) stability and emissions was studied. Then sensitivity of IMEP stability, to change in injection timing and quantity in any of ten transition cycles was systematically studied to see which cycles have the dominant effect on the IMEP stability. A Fast Flame Ionization Detector (FFID) which could measure hydrocarbon concentration with Crank Angle Degree (CAD) resolution, was implemented to measure cycle by cycle variation of EGR as well as engine emissions during mode transition.Results showed that for mode transition from LTC to conventional mode, gradual nonlinear shift in injection timing and quantity is beneficial and the shift should be preferably done when injection timing is advanced and EGR level is high. It was also found that for smooth mode transition injection quantity should be reduced for some cycles to a level below start and end level. The finally achieved injection strategy showed considerable improvement in stability and emissions as Coefficient of Variation (COV) of IMEP across the mode transition was reduced by 8% points and HC emission was reduced by 41% compared to the case with simple abrupt shift in injection timing and quantity.