As a universal phenomenon in nature, capillary rise not only strongly influences the physical properties and industrial processes of powder materials but can also be applied as an important technique to measure their wettability. In this paper, molecular dynamics (MD) was implemented to investigate the capillary transport behavior of water flow through α-quartz nanochannels considering the channel height. The results showed that the Capillary rise method (CRM) with the classical Lucas-Washburn (L-W) equation may obtain an overestimated equilibrium contact angle, and the value decreases with increasing channel height. Through the introduction of the concepts of effective viscosity, slip length and dynamic contact angle, a modified L-W equation was proposed. The equilibrium contact angle calculated by the equation was more accurate and independent of channel size. Additionally, the pore-water can be divided into absorption water and capillary water. The upper bound of the absorption water density was determined to be 1.14 g/cm3.