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Resident memory T (Trm) cells which are specifically located in non-lymphoid tissues showed distinct phenotypes and functions compared to circulating memory T cells and were vital for the initiation of robust immune response within tissues. However, the heterogeneity in the transcriptional features, development pathways, and cancer response of Trm cells in the small intestine was not demonstrated. Here, we integrated scRNA-seq and scTCR-seq data pan-tissue T cells to explore the heterogeneity of Trm cells and their development pathways. Trm were enriched in tissue-specific immune response and those in the DUO specially interacted with B cells via TNF and MHC-I signatures. T cell lineage analyses demonstrated that Trm might be derived from the T_CD4/CD8 subset within the same organ or migrated from spleen and mesenteric lymph nodes. We compared the immune repertoire of Trm among organs and implied that clonotypes in both DUO and ILE were less expanded and hydrophilic TRB CDR3s were enriched in the DUO. We further demonstrated that Trm in the intestine infiltrated the colorectal cancer and several effector molecules were highly expressed. Finally, the TCGA dataset of colorectal cancer implied that the infiltration of Trm from the DUO and the ILE was beneficial for overall survival and the response to immune checkpoint blockade. Highlights: The result uncovers the heterogeneity of tissue-resident memory T cell subsets of distinct intestine organs. The result uncovers the heterogeneity of the differentiation pathways of tissue-resident memory T cell subsets of distinct intestine organs which might be derived from the T_CD4/CD8 subset within the same organ or migrated from distinct organs. T cells from jejunum lamina propria (JEJLP) and jejunum epithelium (JEJEPI) showed overlapped clonotypes which were more clonally expanded. Tissue-resident memory T cell subsets of DUO and ILE in cancer showed acute immune response as well as apoptotic processes. The infiltration of tissue-resident memory T cell subsets of DUO and Ileum (ILE) benefited the overall survival of the colorectal cancer patient. The infiltration of tissue-resident memory T cell subsets of DUO and Ileum (ILE) benefited the response of the immune checkpoint blockade therapy of the colorectal cancer patient. [ABSTRACT FROM AUTHOR]