This paper investigates how industrial structure upgrading influences regional coordination in the digital era, using data from 253 Chinese prefecture-level cities between 2011 and 2021. The research employs a double machine learning model and constructs a Gini coefficient to quantify intracity disparities. Findings indicate that industrial structure upgrading reduces regional disparities overall, with stronger effects during the rapid digital economy development phase. However, in the initial phase of digital infrastructure construction, upgrading intensified disparities due to uneven access to resources and technologies. The analysis also reveals heterogeneity: cities with advanced industrial structures benefit from enhanced coordination, while those with underdeveloped structures face widened disparities. Digitalization moderates these effects by fostering innovation diffusion and improving resource distribution. This paper offers insights into how digitalization and industrial upgrading interact to influence regional coordination, providing a basis for tailored policies to achieve balanced and sustainable urban development.