This work presents a numerical study that investigates the optimum post-injection strategy and internal exhaust gas recirculation (iEGR) application with intake valve re-opening (2IVO) aiming to optimize the brake specific nitric oxide (bsNO) and brake specific soot (bsSoot) trade-off with reasonable brake specific fuel consumption (BSFC) via 1D engine cycle simulation. For model validation, single and post-injection test results obtained from a heavy-duty single cylinder diesel research engine were used. Then, the model was modified for 2IVO application. Following the simulations performed based on Latin hypercube DoE; BSFC, bsNO and bsSoot response surfaces trained by feedforward neural network were generated as a function of the injection (start of main injection, post-injection quantity, post-injection dwell time) and iEGR (2IVO dwell) parameters. After examining the effect of each parameter on pollutant emission and engine performance, multi-objective pareto optimization was performed to obtain pareto optimum solutions in the BSFC-bsNO-bsSoot space for 8.47 bar brake mean effective pressure (BMEP) load and 1500 rpm speed condition. The results show that iEGR and post-injection can significantly reduce NO and soot emissions, respectively. The soot oxidation capability of post-injection comes out only if it is not too close to the main injection and its efficiency and effective timing are substantially affected by iEGR rate and main injection timing. It could also be inferred that by the combination of iEGR and post-injection, NO and soot could be reduced simultaneously with a reasonable increase in BSFC if start of main injection is phased properly.