Molecular dynamics simulation can directly model the molecular behavior, making it convenient to investigate the microscopic mechanism of thermal conductance of boron nitride (BN) nanomaterials. However, there still no explicitly investigation to the size effect of the BN monolayer on its thermal properties. In this paper, the equilibrium molecular dynamics (EMD) combined with the Green-Kubo method was used to unravel and explain the relations between the system size and the thermal conductivity, phonon dispersion, and phonon density of states (DOS) of pristine BN monolayer. It was found that the thermal conductivity of the BN monolayer decreased with increasing the size of the sturcture, reaching a converged value (349±22) W/(m?K) at 4.1 nm×4.1 nm. This value was much smaller than the converging size (10 nm×10 nm) of graphene in calculating its thermal conductivity using EMD simulations, which implied the phonon-phonon scattering in BN monolayer was larger than that in graphene. Different from the thermal conductivity, the phonon dispersion and phonon DOS of the BN monolayer did not depend on the size of the structure. Our findings provide important reference for investigating the microscopic mechanisms of BN related materials by using the equilibrium molecular dynamics modeling.