A comprehensive tolerancing system is presented with its design principle, system architecture and key functions. The following functional modules, automatic generation of dimension chain, equivalent variational mechanism (EVM) modeling and visualized 3D tolerance analysis, are described in detail. Design intent is expressed by assembly tolerance specifications, which may be added to the model and used in computing predicted quality levels. A comprehensive method, based on equivalent replacement, has been developed for modeling variations in 3D mechanical assemblies. The models are constructed of common engineering elements: dimension chain, kinematic joints, assembly datums, dimensional and geometric feature tolerances, and assembly tolerance limits. The method is consistent with engineering design practice and is well suited for integration with commercial CAD systems. To make the tolerancing system robust and efficient, new functionalities are added to well-known CAD software and simulation environment. Tested by many samples, this system shows good robustness and practicability.