Water infiltration through soil particles is of great importance in determining the availability of elements and soil texture. However, process of water infiltrate into the capillary nanochannels and influence of nanochannel size and cation type as well as the underlying mechanism are still lacking, especially at the molecular level. Here, molecular dynamics simulation was used to investigate the infiltration of NaCl and CaCl2 solutions through 1.5, 3, 5, and 10 nm illite channels. At the initial stage, obvious regression of the advanced frontier of salt solution was observed. Water molecules and cations easily accumulated at the entrance of nanochannels, which was clearer in small-sized nanochannels. The infiltration velocity increased with increasing nanochannel size, though time for water saturating the illite nanochannel showed an opposite trend. Both Na+ and Ca2+ exhibited obvious inner-sphere adsorption during the infiltration, but Ca2+ showed more outer-sphere adsorption compared to Na+. Diffusion coefficients of both water and cations were higher in the small- than large-sized nanochannel, which was related to the unsaturated condition, capillary force, and interplay between illite-water interaction and surface tension. By using MD method, this study is the first time, to our knowledge, to investigate the unsaturated capillary infiltration of water in clay soil nanochannels, which is hard to achieve using traditional experimental tools. Results showed that, besides the generally considered interaction between soil particles, cation-clay interactions coupled with nanochannel size were of great importance in affecting the unsaturated infiltration of water and cations. This study provides a new clue in understanding the availability of soil water and stability of soil aggregates.