In this study, we propose a novel federated learning (FL) approach that utilizes 3D style transfer for the multi-organ segmentation task. The multi-organ dataset, obtained by integrating multiple datasets, has high scalability and can improve generalization performance as the data volume increases. However, the heterogeneity of data owing to different clients with diverse imaging conditions and target organs can lead to severe overfitting of local models. To align models that overfit to different local datasets, existing methods require frequent communication with the central server, resulting in higher communication costs and risk of privacy leakage. To achieve an efficient and safe FL, we propose an Anatomical 3D Frequency Domain Generalization (A3DFDG) method for FL. A3DFDG utilizes structural information of human organs and clusters the 3D styles based on the location of organs. By mixing styles based on these clusters, it preserves the anatomical information and leads models to learn intra-organ diversity, while aligning the optimization of each local model. Experiments indicate that our method can maintain its accuracy even in cases where the communication cost is highly limited (=1.25% of the original cost) while achieving a significant difference compared to baselines, with a higher global dice similarity coefficient score of 4.3%. Despite its simplicity and minimal computational overhead, these results demonstrate that our method has high practicality in real-world scenarios where low communication costs and a simple pipeline are required. The code used in this project will be publicly available.