As an important energy base in China, the high-quality development of the Yellow River Basin plays an important role in achieving the goal of "carbon peak and carbon neutrality" in China. Based on the theoretical framework of industrial structure, environmental regulation and carbon emission, a panel vector autoregressive model is adopted to examine the dynamic relationship between environmental regulations, carbon emissions, and industrial structure with the panel data of 79 prefecture-level cities in the Yellow River Basin from 2004 to 2019. The findings indicate that: (1) On the whole, the effect of environmental regulation on carbon emissions is initially boosted, then prevented. Industrial structure has an inhibitory influence on carbon emissions, but this inhibitory effect is with apparent lag. Environmental regulation prevents industrial structure upgrading in the near term. (2) From the regional viewpoint, it can be seen that the degree of coordination between the upper, middle and down reaches of the Yellow River Basin steadily diminishes from east to west during the period of 2004-2019. The down reaches areas basically achieved the coordinated development of among the three. In the middle reaches, the environmental regulation has the most obvious effect on reducing carbon emissions reduction, but the incentive effect on industrial structure upgrading is not obvious, and industrial structure upgrade is clearly insufficient to reduce carbon emissions. In the upper reaches, the effect of industrial structure upgrading on carbon emission reduction is clear, but the effect of environmental control on carbon emission reduction is significantly less than that of industrial structure upgrading. Finally, this study puts forward concrete policy recommendations to achieve the high-quality development in the Yellow River Basin.