In view of the increasingly stringent emission regulations, the automotive sector needs considerable support from the development of robust and reliable engine and aftertreatment models. Accurate reproduction of engine-out and tailpipe pollutants plays a crucial role in complying with these legislations. Given the difficulty in characterizing some critical phenomena, frequently caused by strong dynamics and related to experimental uncertainties, communication between several calibrated and reliable models is mandatory. This is certainly valid for powertrains that will be powered with alternative gas fuels such as natural gas, bio-methane and hydrogen in the future. This paper describes a methodology to co-simulate a 1D CNG HD 6-cyl engine model and a 1D quasi-steady three-way catalyst model in a global framework for high-fidelity virtual prototyping of the vehicle system. Through the implementation of a dedicated control logic in MATLAB/Simulink, the modeling architecture allows for the reproduction of the engine performance parameters together with the evaluation of the TWC pollutants’ conversion efficiency. An extensive database of experimental tests was used to assess the model response. The latter was validated in multiple steady-state operating conditions of the engine workplan. Using a semi-predictive combustion model, the validation was carried out over a wide range of different air-to-fuel ratios and during fast rich/lean transitions to evaluate the formation and conversion phenomena of the main chemical species, both engine-out and tailpipe. Subsequently, the complete model was validated in dynamic conditions throughout a WHTC, accurately reproducing the cut-off phases and their sudden accelerations. The numerical–experimental agreement on pollutant reproduction is generally good and globally below 3%. Larger deviations occur in extremely rich conditions and in CH4 emission evaluation due to the lack of information related to the combustion process and chemical mechanisms involving the Pd surface.