In a quantum dot solar cell (QDSC) that has an inverted structure, the QD layers form two different junctions between the electron transport layer (ETL) and the other semiconducting QD layer. Recent work on an inverted-structure QDSC has revealed that the junction between the QD layers is the dominant junction, rather than the junction between the ETL and the QD layers, which is in contrast to the conventional wisdom. However, to date, there have been a lack of systematic studies on the role and importance of the QD heterojunction structure on the behavior of the solar cell and the resulting device performance. In this study, we have systematically controlled the structure of the QD junction to balance charge transport, which demonstrates that the position of the junction has a significant effect on the hysteresis effect, fill factor, and solar cell performance and is attributed to balanced charge transport.