Insights into the formation mechanisms of two-dimensional covalent organic frameworks (2D COFs) at both the in-plane and interlayer levels are essential for improving material quality and synthetic methodology. Here, we report the controllable preparation of 2D COF films via on-surface synthesis and investigate the growth mechanism using atomic force microscopy. Monolayer, bilayer, and layer-plus-island multilayer COF films were successfully constructed on hexagonal boron nitride in a controlled manner. The porphyrin-based COF films grow in the Stranski-Krastanov mode, i.e., a uniform bilayer COF film can be formed through layer-by-layer growth in the initial stage followed by island growth starting from the third layer. Furthermore, fluorescence quenching caused by π-π stacking interactions between 2D COF neighboring layers was revealed. These results provide new perspectives on the synthesis of high-quality 2D COF films with controllable thickness and morphology, paving the way for a diverse range of applications.