The Yellow River Delta (YRD) is a vital agricultural and ecologically fragile zone in China. Understanding the spatial pattern and evolutionary characteristics of Rural Settlements Area (RSA) in this region is crucial for both ecological protection and sustainable development. This study focuses on Dongying, a key YRD city, and compares four advanced deep learning models—U-Net, DeepLabv3+, TransUNet, and TransDeepLab—using fused Sentinel-1 radar and Landsat optical imagery to identify the optimal method for RSA mapping. Results show that TransUNet, integrating polarization and optical features, achieves the highest accuracy, with Precision, Recall, F1 score, and mIoU of 89.27%, 80.70%, 84.77%, and 85.39%, respectively. Accordingly, TransUNet was applied for the spatiotemporal extraction of RSA in 2002, 2008, 2015, 2019, and 2023. The results indicate that medium-sized settlements dominate, showing a “dense in the west/south, sparse in the east/north” pattern with clustered distribution. Settlement patches are generally regular but grow more complex over time while maintaining strong connectivity. In summary, the proposed method offers technical support for RSA identification in the YRD, and the extracted multi-temporal settlement data can serve as a valuable reference for optimizing settlement layout in the region.