In recent years, 3D Gaussian Splatting (3D-GS)-based scene representation demonstrates significant potential in real-time rendering and training efficiency. However, most existing methods primarily focus on single-map reconstruction, while the registration and fusion of multiple 3D-GS sub-maps remain underexplored. Existing methods typically rely on manual intervention to select a reference sub-map as a template and use point cloud matching for registration. Moreover, hard-threshold filtering of 3D-GS primitives often degrades rendering quality after fusion. In this paper, we present a novel approach for automated 3D-GS sub-map alignment and fusion, eliminating the need for manual intervention while enhancing registration accuracy and fusion quality. First, we extract geometric skeletons across multiple scenes and leverage ellipsoid-aware convolution to capture 3D-GS attributes, facilitating robust scene registration. Second, we introduce a multi-factor Gaussian fusion strategy to mitigate the scene element loss caused by rigid thresholding. Experiments on the ScanNet-GSReg and our Coord datasets demonstrate the effectiveness of the proposed method in registration and fusion. For registration, it achieves a 41.9\% reduction in RRE on complex scenes, ensuring more precise pose estimation. For fusion, it improves PSNR by 10.11 dB, highlighting superior structural preservation. These results confirm its ability to enhance scene alignment and reconstruction fidelity, ensuring more consistent and accurate 3D scene representation for robotic perception and autonomous navigation.