Post‐synthetic modification plays a crucial role in precisely adjusting the structure and functions of advanced materials. Herein, we report the self‐assembly of a tubular heterometallic Pd3Cu6L16 capsule, incorporating Pd(II) and CuL1 metalloligands. This capsule undergoes further modification with two tridentate anionic ligands (L2) resulting in a bicapped Pd3Cu6L16L22 capsule with an Edshammer polyhedral structure. By employing transition metal ions, acid, and oxidation agents, the bicapped capsule is convertible to an uncapped one. This uncapped form can then revert to the bicapped structure with the addition of Br‐ ions and a base. Interestingly, introducing Ag+ leads to the removal of one L2 ligand from the bicapped capsule, yielding a mono‐capped Pd3Cu6L16L2 structure. Furthermore, the size of anions critically influences the precisely controlling the post‐synthetic modifications of the capsules. It was demonstrated that these capsules selectively encapsulate the tetrahedral anions, offering a novel approach in the design of intelligent molecular delivery systems.