Introduction: The manufacturing industry is an important component of urban economy, and its spatial configuration profoundly influences its urban planning, infrastructure development, resource allocation, and sustainable development. A scientific industrial layout can effectively promote the growth, transformation, and upgrading of regional economies. Objectives: Based on data for manufacturing enterprises in Fujian Province spanning 2009–2021, this study explores the spatial distribution patterns of general and innovative manufacturing enterprises at different scales and the factors affecting their spatial distribution. Methods: we conduct spatial statistical analysis using standard deviation ellipse, spatial autocorrelation, kernel density, and negative binomial regression. Results: 1) The spatial distribution of manufacturing enterprises is uneven, mainly distributed along coastal urban belt centered on Ningde, Fuzhou, Quanzhou, Xiamen, and Zhangzhou. General manufacturing has been centered on Quanzhou–Xiamen, while innovative manufacturing centers have shifted from Xiamen to Quanzhou. 2) There are significant spatial agglomeration characteristics, forming two core hotspot areas of Xiamen–Zhangzhou–Quanzhou and Fuzhou. However, innovative manufacturing enterprises exhibit stronger polarization and diffusion phenomena. 3) The spatial pattern evolves from a “point-axis” pattern to a “point-cluster belt” pattern, with stronger spillover effects observed for innovative manufacturing enterprises. 4) The factors affecting the spatial pattern of manufacturing enterprises in Fujian Province show significant changes. Among them, regional distance to ports, industrialization level, financial support strength, transportation accessibility, and population size have significant effects. But the coefficient of distance to ports decreases sharply, external development level changes from having a significant positive effect to not have an effect. Furthermore, patent R&D and the number of economic development zones have more significant effects on innovative manufacturing enterprises. Conclusions: Compared to other coastal provinces in eastern China, Fujian Province's manufacturing industry is more concentrated in coastal areas, and with the industrial transformation and upgrading, the demand for high-quality workers is increasingly strong. Fujian Province should further integrate into the global industrial chain, strengthen industrial clusters, accelerate the cultivation of high-quality talents, thereby promoting high-quality development of the manufacturing industry.