Trace boron in seawater, usually presented as boric acid (B(OH)3), should be firstly transformed into ionic state, in desalination plants, which represents high energy consumption and high cost. Therefore, direct removal of B(OH)3 is significant and energy-efficient for industrial boron removal, which is still a great challenge. A very recent work [Desalination, 533 (2022) 115755] provides strong theoretical guidance on making efficient boron removal devices utilizing 2D materials with hydrophilic pores. However, limited effort has devoted to explore other 2D porous membrane aiming at further improving the performance of boron acid removal. Herein, using molecular dynamics (MD) simulation, we investigated the effect of single-layered graphene nanosheet embedded with hydrophilic crown nanopores on the direct removal of boric acid. We construct six typical graphene crown pores with varied pore dimensions. Our MD results demonstrate that the utilized graphene crown pores show high water permeability, simultaneously accompanied by an outstanding B(OH)3 rejection (mostly over 90%). The water permeabilities through the crown pores achieve a highest value of 6.01 L cm−2 day−1 MPa−1. Remarkably, the water fluxes in each pore are evaluated to be 2.15 ∼ 20.1 × 1013 per day per MPa per pore, featuring 1–2 orders of magnitude improvement compared with the previous best report of 2-dimensional nanopores, with the comparable B(OH)3 rejection. Free energy calculations indicate that a water molecule is energetically more favorable to transport through graphene crown nanopore than B(OH)3. Our findings highlight that a porous graphene embedded with hydrophilic crown nanopores can be not only used for efficaciously removing B(OH)3 but also enable the fast water flow, which is desirable in desalination plants.