It is well known that 3D CFD simulations can give detailed information about fluid and flow properties in complex 3D domains while 1D CFD simulation can provide important information at a system level, i.e. about the performance of the entire engine. The drawbacks of the two simulation methods are that the former requires high computational cost while the latter is not able to capture complex local 3D features of the flow. Therefore, the two simulation methods are to be seen as complementary, indeed a coupling of the two approaches can benefit from the pros of the two methods while minimizing the cons. In particular, with a multi-scale modeling approach (1D-3D) it is possible to simulate large and complex domains by modeling the complex part with a 3D approach and the rest of the domain with a 1D approach. This paper describes an optimization cycle analysis of the unsteady flow of a single cylinder, two stroke gasoline engine using advanced numerical tools, which are in turn validated by means of experimental measurements. In particular, a 3D model (based on STAR-CD code) of the entire engine and a 1D-3D integrated fluid dynamics model (based on GT-POWER 1D and Converge-LITE 3D codes) is developed and applied for the representation of the geometrical domain and for the prediction of performance and gasdynamics in the whole intake and exhaust systems. The methodology allows users to accurately predict and deeply understand unsteady phenomena in the whole engine and capture the wave motion, which strongly affects the muffler 3D design in small two stroke engines equipped with resonance pipes.