Functional properties of nanomaterials strongly depend on their surface atomic structures, but they often become largely different from their bulk structures, exhibiting surface reconstructions and relaxations. However, most of the surface characterization methods are either limited to 2D measurements or not reaching to true 3D atomic-scale resolution, and single-atom level determination of the 3D surface atomic structure for general 3D nanomaterials still remains elusive. Here we demonstrate the measurement of 3D atomic structure at 15 pm precision using a Pt nanoparticle as a model system. Aided by a deep learning-based missing data retrieval combined with atomic electron tomography, the surface atomic structure was reliably measured. We found that <100> and <111> facets contribute differently to the surface strain, resulting in anisotropic strain distribution as well as compressive support boundary effect. The capability of single-atom level surface characterization will not only deepen our understanding of the functional properties of nanomaterials but also open a new door for fine tailoring of their performance. Precise determination of surface atomic structure of metallic nanoparticles is key to unlock their surface/interface properties. Here the authors introduce a neural network-assisted atomic electron tomography approach that provides a three-dimensional reconstruction of metallic nanoparticles at individual atom level.