Objective To investigate non-tuberculous mycobacterial (NTM) infection in hospitalized patients with human immunodeficiency virus (HIV) infection in Kashgar region, providing evidence for early identification and treatment. Methods Data on HIV-infected and non-HIV-infected hospitalized patients with suspected pulmonary tuberculosis and admitted to the First People’s Hospital of Kashi during the same period from January 2020 to June 2025 were analyzed retrospectively. Based on infection types, patients were divided into several groups: HIV co-infected with Mycobacterium tuberculosis (MTB) (HIV/MTB group), HIV co-infected with NTM (HIV/NTM group), non-HIV-infected individuals co-infected with MTB (non-HIV/MTB group), and non-HIV-infected individuals co-infected with NTM (non-HIV/NTM group). Respiratory specimen detection results, clinical symptoms and signs, imaging and laboratory examination indicators, as well as the all-cause mortality during the follow-up period among different groups of patients were compared. The data were analyzed using statistical software SPSS 26.0 and GraphPad Prism 9.0. Results A total of 944 HIV-infected patients were included in the analysis. Respiratory specimens from 152 cases were positive for Mycobacteria, including 141 cases of MTB (92.76%) and 11 cases of NTM (7.24%). Among the 800 non-HIV-infected hospitalized patients with suspected pulmonary tuberculosis during the same period, 440 respiratory specimens were positive for Mycobacteria, including 427 cases (97.05%) of MTB and 13 cases (2.95%) of NTM. NTM positive rate in HIV-infected patients was higher than that in non-HIV-infected patients (P<0.05). Compared with patients in the HIV/MTB group, those in the HIV/NTM group exhibited more cough (81.82% vs 47.52%, P=0.03) and lymphadenopathy (81.82% vs 35.46%, P<0.01), lower CD4⁺T lymphocyte counts (65.00 cells/μL vs 171.00 cells/μL, P=0.04), lower CD4⁺/CD8⁺ratios (0.13 vs 0.37, P<0.01), higher serum albumin (38.10 g/L vs 32.00 g/L, P<0.01), higher nodule rate (72.73% vs 22.70%, P<0.01), and more emphysema (36.36% vs 11.35%, P=0.01). Conclusion In Kashgar region, NTM positive rate among hospitalized HIV-infected patients is higher than that in non-HIV-infected patients. HIV patients co-infected with NTM exhibit more severe immune dysfunction, with higher incidences of cough, lymphadenopathy, emphysema, and pulmonary nodules, as well as elevated all-cause mortality. These clinical features can serve as early identification reference indicators for HIV/NTM co-infection.