For an in-line diesel engine with four cylinder operating in four-stroke mode, the second-order reciprocating inertia forces generally cannot be well balanced with direct approach. The unbalanced second-order inertia forces are the main reason to cause vibration and noise in a diesel engine within low frequency range. The more superior tone quality for modern diesel engine has been expected even for bus application all the time, and there are tougher requirements for truck noise in developed countries, i.e. in Europe and USA. In present research a unique crankshaft system configuration was proposed, which including opposed piston, inner and outer connecting rod, and crankshaft but running in two-stroke mode, to eliminate the second-order inertia force considerably rather than by adding an extra balance shaft mechanism. The theoretical equations that describing self-balancing property of crankshaft system all were obtained based on relevant reasonable assumptions, and then the CAD model was constructed on the basis of optimized results. The multi-body dynamic simulation was also carried out with rigid-flex coupling model. The vibration acceleration was measured at several critical positions in a prototype engine. The comparisons were implemented between conventional diesel engine and opposed piston engine eventually. The results were shown that the special crankshaft system owns tremendous potential to reduce the engine vibration noise clearly as well as owning higher power density, equivalent fuel economy and emission level, compared with a conventional diesel engine.