The process of a cluster-containing water jet impinging on a monocrystalline silicon substrate was studied by molecular dynamics simulation. The results show that as the standoff distance increases, the jet will gradually diverge. As a result, the solidified water film between the cluster and the substrate becomes “thicker” and “looser”. The “thicker” and “looser” water film will then consume more input energy to achieve complete solidification, resulting in the stress region and the high-pressure region of the silicon substrate under small standoff distances to be significantly larger than those under large standoff distances. Therefore, the degree of damage sustained by the substrate will first experience a small change and then decrease quickly as the standoff distance increases. In summary, the occurrence and maintenance of complete solidification of the confined water film between the cluster and the substrate plays a decisive role in the level of damage formation on the silicon substrate. These findings are helpful for exploring the mechanism of an abrasive water jet.