As the largest hydroelectric dam in the world, the Three Gorges Dam (TGD) has raised wide concerns over the environmental and ecological impacts since its dramatic effect on the downstream flow regime of the Yangtze River. Since 2003, the TGD has progressed from the initial operation period to the full operation period, with different effects on the downstream flow regime over each period. Although the upstream inflow change (USIC) of the TGD is a possibly additional factor affecting the downstream flow regime, this has drawn little attention. This study aims to quantify the individual contributions of the TGD and the USIC to the changes of the downstream flow regime over different operation periods of the dam. Using the Muskingum routing model and the Xin'anjiang rainfall–run‐off model, we reconstruct the discharge unregulated by the TGD for the post‐TGD period from 2003 to 2015. On this basis, the effects of the TGD and the USIC on the downstream flow regime are quantitatively assessed. Benchmarked against the flow regime during the pre‐TGD period from 1955 to 2002, it is found that the TGD and the USIC play considerable and comparable roles in affecting the downstream flow regime during the whole post‐TGD period from 2003 to 2015. Furthermore, the TGD appears to have a limited effect on the downstream flow regime during the initial operation period from 2003 to 2008 relative to the USIC. In contrast, during the full operation period from 2009 to 2015, the TGD plays a dominant role in changing the downstream flow regime, although the effect of the USIC cannot be neglected. The findings of this study are helpful to understand the exact impacts of the TGD on the downstream flow regime, thereby facilitating the development of a rational strategy for operating the dam.