© 2019, Tsinghua University Press and Springer-Verlag GmbH Germany, part of Springer Nature. Oriented attachment of nanocrystals is an important route to constructing epitaxially-connected nanocrystal superlattices for various applications. During oriented attachment of semiconductor nanocrystals, neck can be formed between nanocrystals and it strongly influences the properties of the resulting superlattice. However, the neck formation mechanism is poorly understood. Here, we use in situ liquid cell transmission electron microscopy to directly observe the initiation and growth of homoepitaxial necks between PbSe nanocrystals with atomic details. We find that neck initiation occurs slowly (~ 10 s) when two nanocrystals approach to each other within an edge-to-edge distance of 0.6 nm. During neck initiation, Pb and Se atoms defuse from other facets into the gap, forming “dynamic reversible” filaments. Once the filament (neck) width is larger than a critical size of 0.9 nm, it gradually (15 s) widens into a 3-nm-wide neck. The atomic structure of the neck is further obtained using ex situ aberration-corrected scanning TEM imaging. Neck initiation and growth mechanisms are elucidated with density functional theory calculations. Our direct unveiling of the atomic pathways of neck formation during oriented attachment shed light into the fabrication of nanocrystal superlattices with improved structural order and electronic properties. [Figure not available: see fulltext.].