Green fishing vessel is the only way for the future development of fishing vessels. The optimization of mid-section structure of fishing vessels to achieve the goal of energy saving and emission reduction can make it in line with the development trend of fishing vessels. The improved ant colony algorithm is adopted in the optimization design of the mid-section structure of fishing vessel, and 18 sizes including the thickness, sectional area and distance of longitudinal components are selected as design variables to establish objective function of lightweight mid-section longitudinal components as per unit length. According to the Code for Construction of Steel Fishing Vessels (2015), 8 constraints including total longitudinal strength are extracted to establish optimized mathematical model for mid-section structure of fishing vessels. The result of optimization calculation of the model with improved ant colony algorithm shows that the mass of mid-section longitudinal structure of 43m drift netter in cabin length is reduced by 12.43 in total, and the improved ant colony algorithm is more suitable for the structure optimization of fishing vessels. The dead weight of the fishing vessel subject to optimization of mid-section structure is obviously less, the cargo capacity is increased, the economical efficiency of the fishing vessel is improved, and the energy efficiency level of the fishing vessel is improved.