In order to fully implement the Party’s tough fight against poverty, conscientiously implement the policy of targeted poverty alleviation, and accelerate the development of the socialist market economy and the national economy, it is particularly important to strengthen digital information management in the audit of special fiscal poverty alleviation funds. With the continuous advancement of science and technology, the informatization of audit work has become an inevitable trend. However, in the past audit work of special financial funds, it was found that there were a series of problems such as imperfect audit system, weakened audit work, poor audit projects, imperfect supporting facilities, inadequate poverty alleviation funds, slow project progress, and failure to timely check the completion of projects. In order to better realize the timeliness and practicability of audit information of special fiscal poverty alleviation funds and solve the loopholes and deficiencies found in the past, based on the original digital information submanagement system, this paper adopts the J2EE system framework, MVC mode, and B/S security detection system to build a more stable, efficient, and secure financial special poverty alleviation fund management system. After a series of tests, under the premise of effective use of poverty alleviation funds, the system data shows that, from 2012 to 2018, the per capita disposable income of residents in poverty-stricken areas in China increased by 12.1% in nominal terms, an increase of 8.9% compared with 2012, and the gap between the national rural averages has narrowed again.