Currently, the global industrial chain is undergoing accelerated adjustment and reshaping. The security and stability of China’s industrial chain face significant challenges. Enhancing the level of industrial chain modernization will become a key means to promote the high-quality development of the real economy and an urgent requirement to accelerate the development of a Chinese-style modern industrial system. Under the influence of the accelerating changes in the global market, the manufacturing industry has become an important area for achieving industrial chain modernization in the new development pattern. Enhancing modernization level of the industrial chain and promoting high-quality development of the manufacturing industry are of strategic significance for comprehensively building a modern powerful country. An in-depth analysis of the temporal-spatial evolution and spatial correlations of the modernization of manufacturing industry chain can not only provide reference for constructing a high-quality modern industrial system in China but also provide feasible suggestions for achieving coordinated regional development of the modernization of manufacturing industry chain. Based on this, this article constructs a comprehensive index system for the modernization of China’s manufacturing industry chain from four dimensions: innovation, security, high-end, and greenness. The entropy method is used to measure the modernization level of the manufacturing industry chain, and the Dagum Gini coefficient and local Moran index are used to analyze regional differences in the modernization level of the manufacturing industry chain nationwide. The Kernel density estimation and Markov transition probability matrix are used to analyze the evolutionary trend of the development level of the manufacturing industry chain modernization in order to observe its dynamic evolution and steady-state distribution characteristics. The research results show that: First, the modernization of China’s manufacturing industry chain is still at a medium-low level and presents an east high and west low distribution pattern in space. There is a catch-up effect in the eastern region, while the potential in the western region needs to be further explored. Second, overall, the regional differences in modernization level of manufacturing industry chain in China are decreasing, and the gap among provinces is slowly narrowing, with a weakening trend in spatial agglomeration characteristics. Third, the modernization level of manufacturing industry chain in China is constantly improving, but there is a certain degree of middle-income trap and backslide phenomenon. Western provinces and some northeastern provinces have long been at a low level, with significant room for improvement. Obviously, these research conclusions have important reference value for improving the modernization level of manufacturing industry chain. Specifically, considering the current background of supply and demand imbalances and weakening expectations, they provide insights into how to achieve regional coordinated development of the modernization of manufacturing industry chain in China.