Understanding the influence of aspect ratio on water immersion into silica nanoholes is of significant importance to the etching process of semiconductor fabrication and other water immersion-related physical and biological processes. In this work, the processes of water immersion into silica nanoholes with different height/width aspect ratios (ϕ = 0.87, 1.92, 2.97, 4.01, 5.06) and different numbers of water molecules (N = 9986, 19972, 29958, 39944) were studied by molecular dynamics simulations. A comprehensive analysis has been conducted about the detailed process of water immersion and the influence of aspect ratios on water immersion rates. Five distinguishable stages were identified for the immersion process with all studied models. The results reveal that water can easily immerse into the silica nanoholes with larger ϕ and smaller N. The calculation also suggests that aspect ratios have a greater effect on water immersion rates for larger N numbers. The mechanism of the water immersion process is discussed in this work. We also propose a mathematical model to correlate the complete water immersion process for different aspect ratios.