The electronic information manufacturing industry is characterized by a very significant intra-product specialization and can display the characteristics of a regional division of labor. Looking at the existing literature, most studies have mainly examined the position of different countries in the spatial division of labor from the perspective of global value chains, with fewer empirical analyses at the city level or regional scale. Furthermore, deepening the regional division of labor in value chains is an effective way to promote regional industrial synergy and high-quality economic development. Based on the number of listed enterprises and the total number of parent–subsidiary investment connections in the electronic information manufacturing industry, this study reveals the characteristics of the deeper regional division of labor among cities by analyzing the Value Chain Division Index (VCDI). Subsequently, we used the fractional response regression model to analyze influencing factors. We found that, firstly, the core cities are dominated by the production of high-value parts, while the peripheral cities are mainly dominated by the production of middle- and low-value parts. Specifically, northern Anhui, northern Jiangsu, and southwestern Zhejiang are obviously in a disadvantaged position regarding the regional division of labor in the value chain. In the production of middle- and high-value parts, there are close investment connections between the core cities, and only a few peripheral cities maintain a certain degree of connection with the core cities. Therefore, there is a need to further strengthen industrial investment connections between the core and peripheral cities. Secondly, the regional division of labor in the value chain in the Yangtze River Delta region shows the following characteristic: a “one super, many strong” pattern. That is to say, the VCDI value of Shanghai is the highest, and the VCDI value of Suzhou, Ningbo, and Wuxi is also relatively high, while the VCDI value of peripheral cities is relatively low. Furthermore, we found that there is a relatively obvious regional division of labor among cities, but the core cities have strong homogeneity in the high-value areas. Therefore, it is necessary to further strengthen the dislocation of competition between core cities. Thirdly, the model results show that rising land prices and construction in the development zones at the provincial and national levels both have significant contributing effects on the enhancement of the regional division of labor in the value chain, while the innovation inputs, innovation outputs, and their interaction terms show a negative effect. There is a need to further enhance the efficiency of innovation transformation and improve the quality of innovation transformation in order to promote upgrading in the value chain.