Integrating the modern service industry with the advanced manufacturing industry is an important way to cultivate a modern industrial system and achieve high-quality development of economy. This study aims to enhance the supporting and leading role of the Greater Bay Area of Guangdong, Hong Kong, and Macao in China's national economic development and opening up by promoting the in-depth integration of these two industries. A new monitoring system is developed to simulate the level of integration of the modern service and advanced manufacturing industries in the Guangdong–Hong Kong–Macao Greater Bay Area. The dynamic comprehensive evaluation model of stock increment was used to simulate the coupling coordination degree of these two industries. Empirical results reveal that the development of these industries has uneven stock and incremental resource advantages, and their development has not been balanced. The coupling coordination degree of these industries in some areas has become maladjusted, while in other areas, it has fluctuated or developed from coordination to disorderly leap-forward. These findings demonstrate that the study methods and results are significant for analyzing industrial integration processes and promoting in-depth integration development in the Guangdong–Hong Kong–Macao Greater Bay Area. In conclusion, building a monitoring system using the dynamic comprehensive evaluation model of stock increment is an effective way to evaluate the level of integration of these two industries and promote their in-depth integration in the Greater Bay Area.