Objective To investigate the application value of metagenomic next-generation sequencing (mNGS) in pediatric visceral leishmaniasis associated with hemolytic histiocytosis (VL-HLH). Methods Clinical data of children with VL-HLH diagnosed from 1 January 2016 to 30 June 2022 were retrospectively analysed. Results A total of six VL-HLH were enrolled, three cases were imported from other province, and 3 cases were local cases. Clinical manifestations of six cases include fever, splenomegaly, pancytopenia and hyperferremia, five cases combined with hypertriglyceridemia or hypofibrinogenmia., four cases with decreased NK cell activity, three cases with increased sCD25, and two cases with phagocytosis of BMA. The VL-HLH was confirmed by BMA in two cases, and the maximum interval between onset and diagnosis were 62 and 90 days, respectively; other four cases were diagnosed by mNGS, with 34-day (16.0-39.0) interval from onset. There were five cases received glucocorticoid therapy and three cases received chemotherapy due to the delayed diagnosis, and three of them were co-infected. However, two children avoided the chemotherapy for early diagnosis by mNGS, and no co-infection occurred in them. Conclusion The clinical manifestations of VL-CMV are lack of specificity, and it is difficult to diagnose early in endemic areas of non-leishmania. mNGS can provide a basis for early diagnosis of VL-CMV and provide accurate treatment in time.