In order to further improve thermal efficiency and fuel economy, the engine community pays more attention to the advanced controlling strategy. In this paper, the impacts of the continuous variable valve lift (CVVL) system and Miller cycle strategy on the performance behavior of the natural gas spark ignition (SI) engine were comprehensively investigated. The results indicated that pumping loss was decreased, and volumetric efficiency slightly increased with using CVVL. In addition, the intake air mass flow at the intake ports became more smooth, and turbulence flow and its intensity were strengthened with using CVVL, which were beneficial to accelerate combustion rate and improve combustion efficiency. Under the partial load of the 1200 rpm 5 bar, the ratio of the pumping mean effective pressure (PMEP) in indicated mean effective pressure (IMEP) was reduced by 2.74%. Furthermore, an extra 5.43% improvement of indicated thermal efficiency was obtained. On the other hand, peak in-cylinder pressure and peak combustion temperature of the natural gas SI engine operated on Miller cycle were decreased with late intake valve close (LIVC), particularly the pressure and temperature at the end of the compression stroke, which resulted in reducing NOx emissions formation and mitigating knocking combustion. However, the intake mass flow at the intake ports became fluctuation and the volumetric efficiency was decreased with using LIVC. In addition, brake specific fuel consumption was increased and indicated thermal efficiency decreased with employing LIVC.