The System Analysis Module (SAM) is an advanced and modern system analysis tool under development at Argonne National Laboratory for advanced non-LWR reactor safety analysis. It aims to provide fast-running, modest-fidelity, whole-plant transient analyses capabilities, which are essential for fast turnaround design scoping and engineering analyses of advanced reactor concepts. While SAM is being developed as a system-level modeling and simulation tool, advanced modeling techniques being implemented include a reduced-order three-dimensional module, pseudo 3-D conjugate heat transfer modeling in reactor core, flexible and multi-scale modeling of heat transfer between fluid and structures, in addition to the advances in software environments and design, and numerical methods.SAM aims to be a generic system-level safety analysis tool for advanced non-LWRs, including Liquid-Metal-cooled fast Reactors (LMR), Molten Salt Reactors (MSR), Fluoride-salt-cooled Hightemperature Reactors (FHR), and High-Temperature Gas-cooled Reactors (HTGR). SAM takes advantage of advances in physical modeling, numerical methods, and software engineering to enhance its user experience and usability. It utilizes an object-oriented computational framework (MOOSE), and its underlying meshing and finite-element library and linear and non-linear solvers, to leverage the modern advanced software environments and numerical methods.This document provides the theoretical and technical basis of the code to help users understand the underlying physical models (such as governing equations, closure models, and component models), system modeling approaches, numerical discretization and solution methods, and the overall capabilities in SAM. As new code capabilities and features are added, the SAM Theory Manual will be updated periodically to keep it consistent with the state of the development.