To contribute to the design of next-generation high performance and low emission combustion devices, this study provides a series of high fidelity numerical simulations of turbulent premixed combustion and autoignition with different clean fuels. The first part of the thesis consists of the direct numerical simulations (DNS) of the lean hydrogen-air turbulent premixed flames at a wide range of Karlovitz number (Ka) conditions up to Ka = 1,126. Turbulence-chemistry interaction is discussed in terms of statistical analysis of the turbulent flame speed and flame structure. Global and local flame speed are separately studied through the fuel consumption speed and displacement speed of the flame front, respectively, and the results are compared with the reference laminar flames as well as similar studies in the literature. The global flame structure is assessed via cross-sectional and conditional averages, and modeling implication is further discussed. Detailed analysis of the local flame structure along the positive and negative curvature is also conducted, providing an understanding of the different behavior of local heat release response. Finally, as the modeling perspectives for Reynolds-averaged Navier-Stokes (RANS) and large eddy simulations (LES), the mean quantities of major species, intermediate species, density, the reaction rate of the progress variable, and heat release rate are assessed in the context of the probability density function (PDF). The second part of the thesis consists of applications of the advanced mathematical tool called the computational singular perturbation (CSP). A skeletal chemical mechanism is developed using the CSP algorithm for the autoignition of methanol and dimethyl ether blends, and the ignition delay time and laminar flame speed are validated for a wide range of mixture conditions. A series of autoignition simulations are carried out in the canonical counter flow mixing layer using the developed skeletal mechanism, and detailed analyses of the autoignition for the methanol and dimethyl ether blends at a wide range of strain rate conditions are provided using the CSP diagnostics tools for a wide range of chemical and fluid combinations.