Abstract Background Hypoxic stress-induced inflammation had been considered to play an important role in the onset and progression of altitude-related illnesses, but the origin of inflammatory cytokines, the specific responding cell types, and molecular mechanisms remain unknown. Mitochondria are responsible for oxygen consumption and recently reported to be the master regulators of inflammation, but it is not clear whether and how mitochondrial organelles sense the hypoxic stress and then control the inflammation. Methods Human subjects and mouse models were exposed to real or simulated altitude of 5500 m. Bone marrow-derived macrophages (BMDMs) and monocyte RAW264.7 cells were cultured under 1% oxygen hypoxic conditions. Myeloid-specific Bmal1 knock-out mice were generated by crossing Bmal1 flox/flox mice with Lyz2-Cre mice. Inflammation was investigated by assessing inflammatory mediators, monocyte activities, and leukocyte infiltrating. Mitochondrial unfolded protein response was examined by measuring stress markers, such as LONP1, AFG3L2, and HSP60. The target molecular mechanisms were identified by performing bioinformatic analyses, ChIP assays, and gain/loss-of-function experiments. Results 1) Monocytes in peripheral blood mononuclear cell (PBMCs) were more sensitive and contributed promptly to circulating inflammation in response to acute hypobaric hypoxia. 2) Hypoxic stress triggered the mitochondrial unfolded protein response and then induced the mito-inflammation (NLRP3 inflammasome) in monocytes. 3) Activation of Bmal1 drove mitochondrial stress and mito-inflammation by promoting Fis1-mediated mitochondrial fission in monocytes under hypoxia. 4) BHLHE40, a stress-responsive transcription factor directly targeted by HIF-1α, stimulated Bmal1 transcription in monocytes under hypobaric hypoxia. 5) Myeloid-specific Bmal1 deletion alleviated systemic circulating and vascular inflammation under acute hypobaric hypoxia. Conclusion BHLHE40, a transcription factor associated with hypoxia, stimulated Bmal1 , which in turn triggered the mitochondrial unfolded protein response and drove the mito-inflammation in monocytes by promoting Fis1-mediated mitochondrial fission. Our work provides a novel mechanism which may develop the circadian targeting drugs for altitude or hypoxia-related diseases.