The operation process of engineering projects is essentially a process of information flow and processing, which is complex and uncertain. It is necessary to fully consider the subjective initiative characteristics such as the behavioral preferences of the decision-making subjects. However, traditional decision-making methods are based on the assumption of complete rationality but ignore the reality of limited rationality caused by individual psychological factors. Especially in group decision-making, the preference differences among multiple subjects are prone to cause result deviations. Therefore, in the face of the challenges of uncertainty, complexity and the integration of opinions in the operation of engineering projects, this paper constructs an engineering project operation evaluation method that integrates behavioral decision-making characteristics, providing decision support for the improvement of engineering project operation management. Traditional decision-making methods express preferences through language, but they are difficult to capture dynamic psychological changes, resulting in evaluation biases. Meanwhile, as the scale of the participating entities expands, the operation and investment decision-making of engineering projects has gradually evolved into a large-scale group decision-making problem involving the interests of multiple parties, which puts forward higher requirements for the rationality of the decision-making process.