Human lung is a complex organ susceptible to various diseases. Single-cell transcriptomic studies provide rich data for addressing specific research questions. Here, we present uniLUNG, the largest lung transcriptomic cell atlas, comprising over 10 million cells across 20 disease and healthy groups. By assembling a universal hierarchical annotation framework and performing a comprehensive data integration benchmarking, we established standardized lung cell nomenclature and marker genes. Using uniLUNG, we identified Lym-monocytes and T-like B cells, new cell types in certain lung diseases, confirming their existence by comparing with external single-cell atlases. Additionally, we discovered the NSCLC-like SCLC, a transitional malignant cell population related to NSCLC-to-SCLC transition, which was validated and characterized in spatial dimensions, revealing its complex role in tumour progression. Overall, uniLUNG provides an extensive representation of human lung cell diversity and serves as an invaluable data resource and a solid foundation for lung research.

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