Planting trees on a floodplain along a river is a practical and ecological method for embankment protection. Optimization of wave break forest is also a new concept on wave attenuation studies. In this study, we carried out physical experiments to obtain fundamental data and proposed the Cluster Structure Preserving Based on Dictionary Pair for Unsupervised Feature Weighting model (CDUFW) for multi-objective wave break forest design. Physical experiments were designed with considering the effects of different planting configurations on wave attenuation in three scenarios: (1) the equilateral triangle arrangement with different row spacings; (2) different arrangements with the same density; (3) different tree shapes with the same row spacing. The physical experiment condition was typically defined according to the field research of the study area. Then, a multi-objective weighting model for wave break forest design optimization was based on the scheme set of physical experiment outputs using the proposed CDUFW model. Physical experiments showed that different arrangement modes take advantage of the wave attenuation effect of different forest widths. The CDUFW model performed well in finding the effective, economic and reasonable scheme. The proposed model is excellent in data mining and classification, and can be applied to many decision-making and evaluation fields.