Understanding the factors affecting the shape instability of 3D-printed foods when subjected to thermal processing is vital to improve the practicability of 3D food printing. This study investigated the geometrical attributes and baking conditions along with the rheological properties of cookie dough. Various kinds of 3D-printed shapes were processed under different baking conditions (time and temperature). The results demonstrate the relationships between geometry, infill density, and structural deformation due to baking. In conjunction with the known benefits of compositional optimization of cookie dough, the geometrical properties and baking conditions are critical to their resistance to deformation. High-temperature cooking resulted in cracks between the layers. Both the geometrical properties of the designed shapes and baking conditions determined the final quality of the baked cookies. This study established a novel 3D printing method to prepare cookies with various shapes that are resistant to post-processing collapse, which enlightens the 3D printing of future foods.