The endoplasmic reticulum (ER) is physically connected to the cell nucleus via junctions with the nuclear envelope (NE). These ER-NE junctions are essential for supplying the NE with lipids and transmembrane proteins that are synthesized in the ER. Despite the important role of ER-NE junctions, their biogenesis, architecture and maintenance across the cell cycle has remained elusive. In this study, by combining live cell imaging with quantitative three-dimensional electron microscopy, we systematically elucidated the ultrastructure of ER-NE junctions in mammalian cells. We discovered that ER-NE junctions exhibit a constricted hourglass shape that is different from the junctions within the ER. When ER-NE junctions are newly built during NE assembly at mitotic exit, their morphology resembles ER-ER junctions, but they become constricted starting in telophase. Altogether, our findings imply novel mechanisms that remodel ER-NE junctions and have functional implications for the lipid and protein traffic that are crucial for nuclear function.