The Baijiu industry is a significant contributor to both the food industry and the light industry. Its high tax characteristics effectively promote the sustainable development of the regional economy. First, the evaluation index system of scientific and technological innovation (STI) and high-quality development of Baijiu industry (HQDBI) were constructed. The entropy-improved CRITIC method was used to measure the weights. Second, the coordination relationship and evolution trend of STI and HQDBI were explored using the coupling coordination model and the Tapio decoupling model. Then, the transfer law and key influencing factors were further investigated using the Markov chain and grey correlation, respectively. The main contribution is the dynamic evolution of the coupling and decoupling relationships from the perspective of multiple Baijiu provinces, and deeply depicts the coordination relationship and evolutionary trends of STI and HQDBI. The results show that: the spatial distribution of the coupling coordination degree shows high values in the east-west and low values in the north-south characteristics. In 2021, a pattern of coordinated development in Baijiu provinces has emerged along the Yangtze River basin. The decoupling state is mainly strong decoupling, but it remains poor in Shanxi. The coordination process is unstable and difficult to achieve leapfrog development. Coordination, sustainability and innovation environment have a greater impact on the coordination of subsystems.