Taking the low-altitude economic data of 30 provinces (autonomous regions and municipalities directly under the Central Government) in China from 2012 to 2023 as the research object, this paper, based on the theory of low-altitude new quality productivity, verifies the impact of low-altitude economy on the construction of a modern industrial system and the mediating role of new quality productivity by using the mediating effect test method. It constructs a benchmark regression model, a spatial effect model and a mediating effect model to analyze the impact of low-altitude economy on the construction of a modern industrial system, and verifies the mediating role of new quality productivity in the process of low-altitude economy promoting the construction of a modern industrial system. The low-altitude economy promotes the construction of a modern industrial system and has a spatial spillover effect; as an intermediary variable, new quality productivity plays an important role in the process of low-altitude economy promoting the construction of a modern industrial system. From the perspective of the relationship between low-altitude economy and the construction of a modern industrial system, it provides a certain reference for relevant decision-makers. This study enriches the theoretical framework of low-altitude economics and offers empirical evidence for policymakers to formulate targeted strategies for fostering high-quality economic development.