This study attempted to identify the effect of optimized intake manifold geometry on the behaviors and emission level of hydrogen compressed natural gas (H2CNG) fueled engine. For this purpose, a commercial Hyundai Sonata spark ignition engine (SIE) is modified to operate with CNG and hydrogen blend. The optimal intake pipe length was predicted using an analytical acoustic method. A new intake manifold is designed and implemented utilizing natural supercharging managed by over-pressure waves acoustic propagation. Several tests are conducted on the engine using the new manifold with a speed range from 1000 to 5000 rpm. Based on various engine speeds, the variation of brake torque (BT), in-cylinder pressure, NOx and CO emissions investigated by using gasoline, CNG and hydrogen CNG blend (HCNG) fueled engines via external mixtures. The first finding of the study is that the novel geometry improves the in-cylinder pressure by 10% at 3500 rpm. However, high engine speeds show a reduction of 14% in NOx and 40% in HC while speeds below 2000 rpm reduce CO by 40%. The second finding is that the new optimized geometry serves to get rid of both the auto-igni-tion and the backfire for high ratio of hydrogen in the blend.