<p>The Pearl River Delta is the main region in China participating in economic globalization. With the widening gap between urban and rural economies, the problem of imbalance in production factors has gradually emerged. To analyze the relationship of production factor imbalance between urban and rural economies in the Pearl River Delta, a group-level Theil index model was constructed. Method: The study utilized the group-level Theil index model, combined with descriptive statistics, correlation analysis, heterogeneity analysis, and robustness tests, to conduct an empirical analysis of the panel data of nine major cities in the Pearl River Delta from 2020 to 2023. There is a significant positive correlation between the various urban and rural economies and production factors in the Pearl River Delta. The regression coefficients of various production factors are 0.299, 0.426, 0.232, 0.473, and 0.328 respectively. This indicates that technological and capital factors have the strongest driving effect on the imbalance of urban and rural economies, while the driving effect of land factors is relatively weakest. At the same time, the industrial structure also has a significant impact on the degree of imbalance of production factors in urban and rural economies. The average coefficients of industry, service industry, and agriculture are 0.347, 0.326, and 0.293 respectively. This suggests that the imbalance problem of urban and rural production factors in the industrial-dominated regions is more prominent than that in the agriculture-dominated regions. The study verified the core characteristics of production factor imbalance through multi-source data and regression analysis, providing reference for research on urban–rural production factor imbalance in other Chinese regions.</p>