Graphene-based two-dimensional (2D) materials are currently a prominent focus in membrane research, yet they face challenges related to precise perforation and regulation of interface activity. Recently, the successful synthesis of 2D fullerene (C60) (Meirzadeh et al., Nature 2023, 613, 71) has expanded the repertoire of available 2D materials. However, its potential for membrane separation remains unexplored until now. In this study, we propose, for the first time, the utilization of 2D C60 for water desalination, leveraging its natural pores to circumvent the perforation challenge and allowing for precise tuning of interface activity. By establishing quantitative relationships between water flux and various operating conditions, this theoretical work can be extrapolated to guide practical desalination processes. Through non-equilibrium molecular dynamics simulations, it demonstrates that pristine 2D C60 exhibits unparalleled water permeance and achieves 100% salt rejection, regardless of operating pressure or the types of salt ions. To enhance desalination performance, we further propose a rational design strategy using endohedral 2D C60 with a positively charged surface, which improves water permeance up to 29.3 L⋅cm−2⋅day−1⋅MPa−1 and simultaneously reduces crystallization and colloidal fouling on the membrane surface by unlocking electrostatic attraction and repulsion forces, respectively. The mechanism behind this exceptional performance is attributed to the existence of well-endowed nanopores that form a connected hydrogen bond network, enabling swift vertical flow of water through the channels. Our findings showcase the exciting prospects of the novel 2D C60 material and provide a compelling new approach to membrane-based desalination, with the potential to revolutionize membrane materials.