Nowadays, one of the main challenges of marine maintenance is how to select an optimum maintenance strategy for each component of the complex ship machinery system. The uncertainty of the parameters is one of the main difficulties encountered. For example, engineers and experts are always questioning the credibility and integrity of the data collected, and historical maintenance records may also be lost during maintenance. The above data asymmetry will also lead to parameter uncertainty, which directly affects the accuracy of the prediction results. This paper proposes a method for determining maintenance types of ship equipment based on uncertainty theory and the Data Envelopment Analysis (DEA) model. Firstly, this paper constructs an uncertain maintenance optimization model (UMOM) based on the classic Data Envelopment Analysis model. Then, we converted the UMOM into an equivalent deterministic model for easy calculation by the uncertainty theory. Finally, a case study is given to verify this model. The results will conclude that the UMOM can meet the need for a reasonable classification of maintenance types of mechanical equipment in a marine system and provide valuable information for systemic management and storage.