Big data contains rich value, and for enterprise management, it is crucial to recognize the role of data science in promoting business growth. In the daily operation process, enterprise information systems continuously accumulate a large amount of data, which is like wealth waiting to be discovered. Deep exploration and analysis of these data can significantly enhance the scientific and accurate decision-making of enterprises, giving them an advantage in market competition. This article focuses on the application challenges and opportunities of big data analysis in digital innovation management, aiming to provide innovative perspectives and strategies for enterprises. Furthermore, this article introduces an information management system that combines deep learning (DL) technology and big data analysis, which can effectively process and analyze data, providing solid support for enterprise decision-making. Experimental results have shown that the system performs well in applications, not only improving data processing speed, but also creating more business opportunities and competitive advantages for enterprises.