Water migration in the gel pore of the calcium silicate hydrate (C-S-H) influences the durability of cement-based material. The water transport in nanoscale gel pore is dramatically different from transport in capillary pore that is governed by the Lucas-Washburn (L-W) function. Coarse grained molecular dynamics (CGMD) is first utilized to model the capillary transport process of water in the 8 nm channel of C-S-H gel. A new capillary transport model is proposed by modifying the classic L-W function, taking into consideration the effects of dynamic contact angle and inertia force, slip length next to interior walls of gel pore and viscosity variation for liquid ultra-confined in nanopores. Theoretical modification reaches reasonable agreement with CGMD results. The effect of pore size on capillary transport is then simulated to confirm the model's transferability. The new model is helpful to understand the transport behavior of liquid in the gel pore of cement-based material.