The location selection mechanism and effect of industrial transfer have been widely considered in academia, but the influence of institutional factors on cross-regional industrial transfer and regional differences still need further investigation. Based on theories of economic geography as well as new economic geography (NEG) and its’ institutional transformation, this paper studies the form, mechanism, and effect of the “core–periphery” regional relationship between the Pearl River Delta (PRD) and non-Pearl River Delta (NPRD) areas in Guangdong Province from the micro perspective of industrial spatial organization. Based on a case study on the change of the cross-regional production spatial organization of ceramics enterprises between Foshan and Qingyuan, it is found that after three rounds of spatial reorganization, the production spatial organization of Foshan’s and Qingyuan’s ceramics industries has changed significantly, forming a multifactory, multilocation production spatial structure and regional production network, which further drives to form the regional functional division of “core–periphery”. Institution factors, especially environmental regulation and industrial transfer institutional arrangements, have become an important driving force for the current industrial transfer, but its impact on regional relations is still not a decisive factor. The path locking of the “core–periphery” mode has not been fundamentally broken through. Although the form of spatial inequality has greatly changed, in fact, it produces a new form of inequality. The economic, geographical, and political theoretical framework from the micro-perspective of enterprises will provide a possible theoretical explanation for the phenomenon of “pollution moving to the West, high-tech industry moving to the East, industrial output gathering to the East” in China.