In small and compact class vehicles equipped with diesel engines, the 2-valve-per-cylinder design still holds a significant share of the market. The current work describes the numerical simulation of port-valve-cylinder flow in a 1.2 liter 2-valve-per-cylinder diesel engine to characterize the performance of its manifold and intake ports. First, evaluation metrics were defined and analysis procedure was established for CFD assessment of intake manifold performance in multi-cylinder engines. Then the CFD analysis was carried out for the 2-valve engine in comparison with the baseline 4-valve reference engine. The results show that a complex interaction between intake port and flow distribution around TDC was found in the 2-valve engine, resulting in much higher mean flow velocity, inhomogeneity index/rotational momentum at the port inlet and consequently higher swirl ratio than the baseline 4-valve engine, which can cause high smoke at high load operations. As the recovery plan, CFD simulations show that the high capacity manifold with bigger plenum volume and longer runners helps improve flow homogeneity and cylinder-to-cylinder flow variations in the 2-valve engine. The benefits in improving engine torque and emissions have been verified by multi-cylinder engine testing.