Geometrically complex timber plate structures using wood-wood connections are increasingly designed thanks to digital fabrication. Whereas their fabrication has been automated using computer-aided design programming, research focused on the development of automated numerical tools for their structural analysis has been very limited. This paper presents a method to automate the generation of a finite element model for the analysis of structures with a large number of joints. The model is developed taking the example of recently developed double-layered timber plate shells. Vertical displacements obtained with the semi-rigid spring model proposed are in good agreement with experimental tests performed on small-scale prototypes, whereas rigid modelling of the connections highly underestimates displacements of the structure. Semi-rigidity of the connections in translation as well as in rotation was shown to highly influence the model. The generation of the numerical model was successfully automated for large-scale structures.