The spatial restructuring of regional manufacturing industry involves the dispersion of different types of industries and change in industrial spatial structure. It is an important driving force for optimizing regional spatial organization and increasing regional competitiveness. Based on the aggregated data of manufacturing enterprises, this study used county as the basic unit of analysis to explore the spatial reconstruction features of manufacturing space in the Pearl River Delta urban agglomeration. The result shows that, the differences in spatial agglomeration and diffusion of different types of manufacturing industries have led to further change of the "core-periphery" structure of the urban agglomeration. Core cities have become more specialized in the development of technology-intensive industries, while peripheral cities have accommodated labor-intensive industries. Resource and environmental carrying capacity has significantly affected the changes in the spatial pattern of manufacturing industry. The shortage of land resources has prompted the manufacturing industry in general and particularly labor-intensive industries to shift to areas with more abundant land resources. Environmental stress has facilitated the proliferation of labor-intensive and capital-intensive industries in places with greater environmental carrying capacity. However, the impact of resource and environmental carrying capacity on technology-intensive industries is not obvious. In addition, the impact of traffic conditions, technological levels, policies, and other factors on different types of industries is significantly different, which jointly promote the industrial transformation of the Pearl River Delta urban agglomeration.