Ion exchange is an effective postsynthesis strategy for the design of colloidal nanomaterials with unique structures and properties. In contrast to the rapid development of cation exchange (CE), the study of anion exchange is still in its infancy and requires an in-depth understanding. Magic-size clusters (MSCs) are important reaction intermediates in quantum dot (QD) synthesis, and studying the ion exchange processes can provide valuable insights into the transformations of QDs. Here, we achieved anion exchange in Cd-based MSCs and elucidated the reaction pathways. We demonstrated that the anion exchange was a stepwise intermolecular transition mediated by covalent inorganic complexes (CICs). We proposed that this transition involved three essential steps: the disassembly of CdE1-MSCs into CdE1-CICs (step 1), an anion exchange reaction from CdE1-CICs to CdE2-CICs (step 2), and assembly of CdE2-CICs to CdE2-MSCs (step 3). Step 3 was the rate-determining step and followed first-order reaction kinetics (kobs = 0.01 min-1; from CdSe-MSCs to CdS-MSCs). Further studies revealed that the activity of foreign anions only affected the reaction kinetics without altering the reaction pathway. The present study provides a deeper insight into the anion exchange mechanisms of MSCs and will further shed light on the synthesis of QDs.