A system and a method analyze fatigue damage of a bottom hole assembly (“BHA”), and more specifically, use a multi-scale approach for fatigue analysis of a BHA. Three length scales may be used in modeling of a BHA, namely the BHA scale, the component scale and the feature scale. Loading conditions for each collar/tool of the BHA may be determined, such as by use of a beam model, and may be applied to the finite element models for the collar/tool to determine the fatigue damage of each fatigue susceptible feature of each collar/tool. A cumulative fatigue damage of each critical feature may be determined, and the weakest component of the BHA may be identified. Prognostic and diagnostic implementation with well survey and drilling data may monitor fatigue damage of critical components of the BHA.