Understanding the capillary filling behaviors in nanopores is crucial for many science and engineering problems. Compared with the classical Bell-Cameron-Lucas-Washburn (BCLW) theory, anomalous coefficient is always observed because of the increasing role of surfaces. Here, a molecular kinetics approach is adopted to explain the mechanism of anomalous behaviors at the molecular level; a unified model taking account of the confined liquid properties (viscosity and density) and slip boundary condition is proposed to demonstrate the macroscopic consequences, and the model results are successfully validated against the published literature. The results show that (1) the effective viscosity induced by the interaction from the pore wall, as a function of wettability and the pore dimension (nanoslit height or nanotube diameter), may remarkably slow down the capillary filling process more than theoretically predicted. (2) The true slip, where water molecules directly slide on the walls, strongly depends on the wettability and will increase as the contact angle increases. In the hydrophilic nanopores, though, the magnitude may be comparable with the pore dimensions and promote the capillary filling compared with the classical BCLW model. (3) Compared with the other model, the proposed model can successfully predict the capillary filling for both faster or slower capillary filling process; meanwhile, it can capture the underlying physics behind these behaviors at the molecular level based on the effective viscosity and slippage. (4) The surface effects have different influence on the capillary filling in nanoslits and nanotubes, and the relative magnitude will change with the variation of wettability as well as the pore dimension.