This article takes water enterprises as the research object, exploring the organic combination of comprehensive budget management under the trend of digitalization and digital technology in the new era, as well as the process of management system reform. Introduce the current status of its budget management work, comprehensively analyze the architecture and operation mode of the current comprehensive budget management system of water enterprises, and evaluate and analyze the overall situation and shortcomings of its budget management system based on financial data such as budget formulation and execution. From the perspective of digital restructuring and upgrading of comprehensive budget management work, corresponding countermeasures are proposed to make up for the shortcomings and suggestions for the future development of the enterprise’s comprehensive budget.