Manufacturing industry is the material foundation of national economy, the traditional supply chain in a single value creation mode makes the manufacturing industry in the global value chain competition in the "low-end lock" predicament, to create a highly efficient, intelligent supply chain, is the manufacturing industry in the global competition to gain an advantage in the key. In the process of "Digital to Intelligent Reform", the matching mechanism and decision-making method of supply chain heterogeneity partner selection is the focus of manufacturing supply chain transformation to be solved urgently. This paper takes the manufacturers and suppliers of manufacturing secondary supply chain as the research object, takes service quality as the important influence factor of partner selection, and explores the supply chain partner matching evaluation model under the three modes of unilateral decision-making, bilateral decision-making, and optimization of bilateral decision-making. The study shows that the bilateral matching decision-making mechanism based on QoS can obtain a higher matching completion rate, while digital transformation helps to improve the efficiency and stability of supply chain partner selection. The study can provide a decision basis for heterogeneous partner selection in manufacturing supply chain, and then improve the overall performance of manufacturing supply chain.