Quasi-continuum water flow under highly confined conditions has tremendous applications in chemical engineering and nanotechnology. For a type of quasi-continuum flow, a bulk phase exists in the middle of a flow region, while the viscosity of water at its boundary is largely affected by a pore wall, and the slippage effect cannot be neglected. In this work, we propose an effective viscosity model based on a classic molecular kinetic theory and apply a slip length model based on a quasi-universal relationship between a contact angle and the slip length. It is found that the effective viscosity of water is highly affected by a wettability condition, and a linear relationship exists between the contact angle and the interfacial viscosity. The main reason for this phenomenon lies in a different magnitude of the Hamaker constant under various wettability conditions. Besides, it is found that the applied slip length model considers most of the factors that affect the slip length, except for the molecular structure of a solid substrate. Furthermore, we analyze how these two factors contribute to the total flow rate under various wettability conditions and apply our theories into a capillary filling process. It is validated that the proposed model can be used to predict the capillary filling behavior.