The nuclear pore complex (NPC) is a critical structure for nucleocytoplasmic transport, and its core architecture has been well-studied. However, the peripheral regions, such as the cage-like nuclear basket, have shown significant variation across different species. This study used in-cell cryo-electron tomography and subtomogram analysis to explore the structural variations of the NPC and the nuclear basket in fungi (yeast), mammals (mouse), and protozoa (T. gondii). The results revealed that a stable basket is associated with a double nuclear ring (NR), and the basket consists of struts emanating from this double NR, terminating in distal densities. The molecular architecture of the yeast and mammalian baskets was modeled using integrative structural modeling, incorporating biochemical data and in-cell maps. The models showed that the basket consists of a NR anchor module, a basket strut module, and a basket distal module. The NR anchor module is positioned near the central channel of the NPC and the NE, while the basket strut module forms the struts of the basket. The basket distal module contains the C-terminal domains of the basket-forming proteins, which may serve as docking sites for mRNA preprocessing. The study also highlighted the presence of an exclusion zone around the basket, suggesting its role in chromatin organization and mRNA surveillance. The findings provide insights into the structural and functional variations of the NPC and the nuclear basket across different species.The nuclear pore complex (NPC) is a critical structure for nucleocytoplasmic transport, and its core architecture has been well-studied. However, the peripheral regions, such as the cage-like nuclear basket, have shown significant variation across different species. This study used in-cell cryo-electron tomography and subtomogram analysis to explore the structural variations of the NPC and the nuclear basket in fungi (yeast), mammals (mouse), and protozoa (T. gondii). The results revealed that a stable basket is associated with a double nuclear ring (NR), and the basket consists of struts emanating from this double NR, terminating in distal densities. The molecular architecture of the yeast and mammalian baskets was modeled using integrative structural modeling, incorporating biochemical data and in-cell maps. The models showed that the basket consists of a NR anchor module, a basket strut module, and a basket distal module. The NR anchor module is positioned near the central channel of the NPC and the NE, while the basket strut module forms the struts of the basket. The basket distal module contains the C-terminal domains of the basket-forming proteins, which may serve as docking sites for mRNA preprocessing. The study also highlighted the presence of an exclusion zone around the basket, suggesting its role in chromatin organization and mRNA surveillance. The findings provide insights into the structural and functional variations of the NPC and the nuclear basket across different species.