Under the continuous promotion of ecological civilization construction and the optimization of national audit function, environmental audit plays a very important role in government audit work, and is still undergoing dynamic changes. This study takes the balanced scorecard theory as the guiding theory, combines the relevance and basic characteristics of green development and government environmental audit, and puts forward the environmental audit index system of the government of the Yangtze River Economic Zone under the perspective of green development. It also utilizes the principal component extraction method and variable-weight hierarchical comprehensive evaluation method to audit and evaluate the government environment. The results of the study show that the government environment of Hubei province in the Yangtze River Economic Belt has the lowest audit score in terms of the quality of green development, with a score of only 60.67%. After the supervision and rectification assisted by the audit system, the government and enterprises realize green governance and green development through environmental protection investment, scientific and technological innovation, and pollution control, and the environmental protection expenditure of the province increases year by year from 2023 to 2024. Carrying out effective environmental audits on the government can not only implement supervision on the work of relevant government departments, but also enhance the environmental awareness of the whole society, and the governmental environmental audit system proposed in this study can, in a sense, promote the implementation of environmental protection programs in the Yangtze River Economic Belt.