Deciphering the spatial organization of macromolecular complexes in their native context is central to structural biology. Particle fusion in single-molecule localization microscopy offers a unique capability for high-resolution structural reconstruction in situ. However, existing methods face significant challenges from large rotational perturbations and sparse labeling, resulting in compromised accuracy and substantial computational cost. We present DeepSRFusion, a self-supervised pretraining framework for three-dimensional super-resolution particle fusion. By representing single-molecule point clouds as Gaussian Mixture Models, DeepSRFusion integrates data-driven feature learning with physical imaging constraints. A two-stage optimization strategy with dynamic template updating enhances robustness, and a novel Clustering Error metric quantifies fusion quality. Nanometer-scale validation on both simulated and experimental datasets demonstrates high reconstruction fidelity and structural consistency with cryo-electron microscopy and AlphaFold3. DeepSRFusion remains effective under challenging imaging conditions, including large 3D rotations, sparse labeling, high localization uncertainty, and limited particle numbers, while achieving over 100-fold speedups compared to current methods. It resolves fine structural features with a measured spatial resolution of ~1.6 nm, sufficient to distinguish ~10 nm spaced protein pairs and visualize tilted internal substructures within macromolecular assemblies. DeepSRFusion provides a powerful tool for high-precision structural analysis in native cellular environments.