The construction of the Chengdu-Chongqing Economic Circle is a major decision and deployment to promote integrated development in China. Based on panel data of the Chengdu Chongqing Economic Circle from 2012 to 2021, this study analyzes the interrelationships among population agglomeration, industrial structure, and regional economic disparities in the Chengdu-Chongqing Economic Circle, as well as their mechanisms by using the benchmark model, the threshold effect model and the mediating effect model. The research results show that population agglomeration significantly narrows the economic disparities among regions in the Chengdu-Chongqing Economic Circle. Population agglomeration has a double-threshold effect on reducing regional economic disparities, with industrial structure as the threshold: when the industrial structure exceeds the corresponding threshold values, the impact of population agglomeration on economic disparities among regions is greater. Population agglomeration also narrows regional economic disparities through the mediating channel of promoting industrial structure upgrading. The conclusions of the study provide valuable insights for optimizing spatial layout and promoting coordinated regional development, as well as achieving balanced development in the Chengdu-Chongqing Economic Circle.