Flood, a natural disaster closely related to global climate change, harms child health. However, the long-term effect of flood exposure on child mortality is unknown, particularly in low- and middle-income countries (LMICs). Here, based on a sibling-matched case-control design and exposure data of 913 large flood events, we first estimate the under-5 deaths (U5Ds) attributable to long-term flood exposure in 100 LMICs, where there are >90% of global U5Ds.