The development and optimization of high‐performance anode materials for alkali metal ion batteries is crucial for the green energy evolution. Atomic scale computational modeling such as density functional theory and molecular dynamics allows for efficient and adventurous materials design from the nanoscale, and have emerged as invaluable tools. Computational modeling cannot only provide fundamental insight, but also present input for multiscale models and experimental synthesis, often where quantities cannot readily be obtained by other means. In this review, an overview of three main anode classes; alloying, conversion, and intercalation‐type anodes, is provided and how atomic scale modeling is used to understand and optimize these materials for applications in lithium‐, sodium‐, and potassium‐ion batteries. In the last part of this review, a novel type of anode materials that are largely predicted from density functional theory simulations is presented. These 2D materials are currently in their early stages of development and are only expected to gain in importance in the years to come, both within the battery field and beyond, highlighting the ability of atomic scale materials design. Computational materials design has greatly accelerated the alkali‐ion battery field. This review shows that computational modeling is an integral part of the battery research environment and a powerful tool to support experimental studies, to unravel important atomic scale properties and features to gain fundamental understanding of properties and mechanisms that are challenging to obtain solely from experimental analysis and measurements.