Soil is the basis for life and soil science is regarded as the final frontier; however, as compared to chemistry, physics, biology, and other disciplines, soil science undergoes an obviously slower development and remains almost stagnant in the past few decades, mainly due to two reasons: (1) wrong and outdated perceptions for a large portion of soil researchers; (2) complexity of soil systems that are difficult to characterize by current experimental techniques. Computer simulations have unique advantages to handle complex systems while currently, its role during soil researches is far from being recognized. In this chapter, several examples are given with respect to application of density functional theory (DFT) calculations to soil science, focusing on the adsorption of uranyl ion and SO 2 onto mineral surfaces and reaction mechanisms to form acid rain. In this way, insightful clues at the atomic level are provided for the adsorption, interaction, and reactions regarding soil systems. We believe that computer simulations including DFT are the right key to unravel the complicated processes occurring in soils. More efforts of computer simulations are anticipated for soil science with aim to decipher the experimental results and probe the uncharted principles that may result in a revolutionary in the near future.