Marine fishery carbon emissions play a significant role in agricultural carbon emissions, making resource allocation a crucial topic for the overall marine ecological protection. This paper evaluates the dynamic iteration method as a research approach with the factors of resource allocation consisting of value assessment, optimization objective, difference between value assessment and objective, and optimization calculation. The paper selects the shadow price from the Super-SBM model as the judgment function for the goal value, aiming for the fairness criterion. From an equity standpoint, the allocation of carbon resources in marine capture fisheries proves to be unreasonable. The fishery model exhibits an excessive supply of carbon resources, resulting in wastage, while the green fishery model faces a relatively limited supply, with a focus on energy conservation and environmental protection. To address this issue, this paper proposes a new method and discusses the corrective results. This result shows that the stabilization point achieved is a short-term equilibrium rather than a long-term one. By rectifying the social contradiction of profit-oriented approaches, this research provides a fresh perspective for economic studies and applications, particularly in industrial layout and resource utilization optimization.