In this paper, a tolerance representation model for generating tolerance specification schemes and corresponding tolerance zones is proposed to meet the requirement of the representation of tolerance information semantics. This model is hierarchically organized and consists of five layers. They are component, geometric feature, variational geometric constraint, tolerance specification scheme, and tolerance zone layers. The mating relations between components in the component layer, the mating relations between geometric features in the geometric feature layer, the variational geometric constraints between geometric features in the variational geometric constraint layer, the tolerance specification schemes of component in the tolerance specification scheme layer, and the tolerance zones of tolerance specification schemes in the tolerance zone layer are formally defined by one or more adjacency matrices, respectively. Based on the model, a method for generating tolerance specification schemes for component and their resultant tolerance zones is designed. This method shows how to adopt a top-down strategy to carry out tolerance specification for an arbitrary assembly designed in a CAD system. The paper also provides a practical example to illustrate how the method works.