Fracture in silicon anodes has fascinated the electrochemistry community for two decades, as it can result in a 80% capacity loss over the first few electrochemical cycles and is the limiting factor in commercializing such high capacity anodes. Although numerous experimental data exist illustrating severe fracture patterns and their dependence on the scale of the microstructure, no theoretical model has been able to re-produce and capture such behaviour. In this article, a multi-physics phase-field damage model is presented that can accurately capture the long standing problem of dry bed-lake crack patterns observed for Si thin film anodes. A promising aspect of the model is that, in addition to accounting for Li-ion diffusion, it can explicitly capture the microstructure, and therefore when applied to a Si film with a thickness below 100 nm no fracture was observed, which is consistent with experiments. As fracture in continuous thin films is random, micron-hole patterned Si films were also fabricated and cycled, resulting in ordered crack patterns. The proposed model was able to capture these elaborate, yet ordered, crack patterns, further validating its efficiency in predicting damage during lithiation of Si. This paves the way to using multiscale modeling for predicting the dimensions that limit and control fracture during lithiation, prolonging hence the electrode lifetime.