The microbiota regulate hematopoiesis in the bone marrow (BM); however, the detailed mechanisms remain largely unknown. In this study, we explored how microbiota-derived molecules (MDMs) were transferred to the BM and sensed by the local immune cells to control hematopoiesis under steady-state conditions. We reveal that MDMs, including bacterial DNA (bDNA), reach the BM via systemic blood circulation and are captured by CX3CR1(+) mononuclear cells (MNCs). CX3CR1(+) MNCs sense MDMs via endolysosomal Toll-like receptors (TLRs) to produce inflammatory cytokines, which control the basal expansion of hematopoietic progenitors, but not hematopoietic stem cells, and their differentiation potential toward myeloid lineages. CX3CR1(+) MNCs colocate with hematopoietic progenitors at the perivascular region, and the depletion of CX3CR1(+) MNCs impedes bDNA influx into the BM. Moreover, the abrogation of TLR pathways in CX3CR1(+) MNCs abolished the microbiota effect on hematopoiesis. These studies demonstrate that systemic MDMs control BM hematopoiesis by producing CX3CR1(+) MNC-mediated cytokines in the steady-state.