Atomically thin monoisotopic hexagonal boron nitride (BN) which is electrically insulating and has a high thermal conductivity could be utilized as fillers in electronic packaging materials for thermal dissipation in integrated and miniaturized modern devices. Thermal expansion mismatch in electronic packaging could cause strain and ultimately device failure, so it is valuable to measure and understand the thermal expansion coefficient (TEC) of atomically thin isotopically pure BN. In this work, we studied the TECs of mono-, bi-, and tri-layer isotope-purified BN using Raman spectroscopy and density functional theory (DFT) calculations including van der Waals dispersion forces. Monolayer (1L) 10BN had a slightly larger experimental TEC than 1L 11BN at close to room temperature: (−5.1±0.8)×10−6/K and (−4.6±0.8)×10−6/K, respectively. The negative TECs up to 700K were attributed to the competition between the in-plane stretching vibration modes and out-of-plane bending modes in BN; the lighter isotope leads to a larger absolute TEC due to higher amplitude of its out-of-plane bending modes. The absolute TECs of isotopic BN decreased with increased atomic thickness, which indicates strengthening of the out-of-plane bending rigidity. The deep understanding of the isotope effect on the TEC of two-dimensional materials also opens a promising pathway to minimize TEC mismatch in two-dimensional van der Waals heterostructures.