Zeolites, crystalline aluminosilicate materials with well-defined porous structures, have emerged as versatile materials with applications in carbon capture. Hydrothermal synthesis is a widely used method for zeolite production, offering control over crystallinity and and pore size. However, the intricate interplay of synthesis parameters necessitates a comprehensive understanding to optimize the synthesis process. We train a supervised classification machine learning model on ZeoSyn (a dataset of zeolite synthesis routes) to predict the zeolite framework product given a synthesis route. Subsequently, we leverage SHapley Additive Explanations (SHAP) to reveal key synthesis-structure relationships in zeolites. To that end, we introduce an aggregation SHAP approach to extend such analysis to explain the formation of composite building units (CBUs) of zeolites. Analysis at this unprecedented scale sheds light on key synthesis parameters driving zeolite crystallization.