When the datum features apply a material condition, the tolerance of a related feature must coordinate with its datum features. The tolerance coordination design of the related feature with its datum features is an important issue; an uncoordinated tolerance will give rise to an unnecessarily tight tolerance of a target geometrical feature or an invalid application of the material condition. In this paper, a coordination design method is proposed. The notion of the shift tolerance is used to establish the coordination relationship of the tolerance between the related feature and its datum features. The calculation mechanism of the shift tolerance for two datum features applying a material condition is described. To calculate the shift tolerance of the datum features, the datum feature simulator is used to construct the measurement coordinate system and the design coordinate system. For the different combination of two datum features applying a material condition, the relative motion of the design coordinate system with respect to the measurement coordinate system is represented by the parallel-crank mechanism, and the length of the crank is used to calculate the shift tolerance. Based on the shift tolerance, two criteria of the tolerance design at applying material condition are studied, one is the coordination guideline for the geometric tolerance of the related feature and the dimensional tolerance of the datum feature; the other criterion is the coordination guideline for the dimension tolerance between two datum features. Finally, two case studies are introduced to verify reasonableness of the proposed criteria and method.