Under the dual background of digitalization and servitization, how manufacturing enterprises can empower service innovation through digital capabilities is a concern shared by both the theoretical and practical communities. Based on the dynamic capabilities theory and organizational information processing theory, the theoretical model of three kinds of digital capabilities affecting the service innovation performance of manufacturing was constructed with organizational agility as the moderating variable. Through the questionnaire survey and empirical analysis of 276 manufacturing enterprises, the result shows three kinds of digital capabilities can significantly promote the service innovation performance of manufacturing enterprises. Two types of organizational agility play a differential moderating role in this process. Market agility enhances the positive relationship between digital perception and service innovation performance of manufacturing enterprises, while operational agility enhances the positive effects of digital insight and digital transformation capabilities on the performance of service innovation in manufacturing enterprises. It enriches the antecedents of service innovation in manufacturing enterprises and provides guidance for the transformation and upgrading of manufacturing enterprises in the era of digital economy.