China is at a critical stage of comprehensively implementing the regional coordinated development strategy, and the integrated development of the Yangtze River Delta has risen to a national strategy. R&D personnel and R&D capital are important strategic resources for implementing innovation driven development and ensuring the improvement of innovation performance in the Yangtze River Delta region. Based on the panel data of innovation factors in the Yangtze River Economic Belt, this paper uses the spatial econometric analysis method to analyze the direction and structural characteristics of the flow of innovation factors in the Yangtze River Delta within the Yangtze River Economic Belt. At the same time, it analyzes the space time correlation of the flow of innovation factors in the Yangtze River Delta and the impact of the flow of innovation factors on innovation performance in Jiangsu Province. The research results show that the flow of R&D personnel in the Yangtze River Delta mainly affects innovation performance through direct effects and spatial spillover effects; the flow of R&D capital affects innovation performance mainly through the resource allocation effect and the spatial spillover effect of capital outflow. On the basis of empirical analysis, combined with the situation of Jiangsu Province, this paper puts forward policy suggestions such as the introduction strategy design of relevant innovation elements that give consideration to the benign economic development of Jiangsu Province and curb the growing inequality in the distribution of innovation elements among regions, further optimize the configuration structure of innovation elements, and promote the high quality economic development of Jiangsu Province.