Of recent concern are the emissions from two-stroke engines including regulated hydrocarbon and oxide of nitrogen emissions. As history dictates non-road engines often adopt prove technologies from the on-road market. For example, four stroke diesel generators now include additional internal exhaust gas recirculation via an intake/exhaust valve passage. EGR can offer benefits of reduced HC, NOx, and may even improve combustion stability and fuel efficiency. In addition, there is particular interest in use of natural gas as fuel for home power generation. We previously converted an engine to operate on natural gas via electronic port fuel injected and implemented tuned intake and exhaust systems to improve power density and efficiency. This paper examines exhaust throttling applied to the Helmholtz resonator of a two-stroke, port injected, natural gas engine. The 29cc engine was air cooled and operated with wide open throttle conditions on the intake at an engine speed of 5400 RPM with fueling adjusted to achieve maximum brake torque. Exhaust throttling served as method to decrease the effective diameter of the outlet of the convergent cone. Throttling balanced energy and exergy flows by acting as a source of internal EGR and lowering combustion temperatures, which yielded lower heat transfer. Though exhaust throttling improved efficiency, it deteriorated power density. Quantification and comparison of trapping and scavenging efficiency has been done by using exhaust and intake gas concentration and temperature. In-cylinder pressure was used to investigate combustion phasing, heat release rate and trapped mass inside of the cylinder. Exhaust throttling had a negative impact on the delivery ratio and positive impact on trapping efficiency inducing back pressure on exhaust port. Also, NOx and THC emissions decreased on throttled cases.