Saline soil is composed of abundant soluble salts, exhibiting undesirable properties when used in backfill projects. To address the mentioned problem, a hydrophobic polymer with an active ingredient of hydrosiloxane-containing siloxane was evaluated as a soil additive in this paper. Five groups of specimens were solidified with a fixed dosage of polymer, with initial water contents (IWCs) ranging from 12.8% to 20.8%, to determine the effectiveness of polymer treatment and the effect of IWC. Natural specimens were also prepared to serve as a control condition. Results showed that the polymer formed a hydrophobic interface on the surface of soil particles, causing the shrinkage of the diffuse double layer (DDL) and the flocculation of clay particles. Therefore, the plasticity index reduced, and the fine particles transformed into coarser particles after polymer treatment. Furthermore, the polymer-solidified soil exhibited a significant enhancement in unconfined compressive strength, characterized by an agglomerated microstructure that possessed a high cementing ability. Nevertheless, increasing IWCs continuously induced a decrease in the strength of the solidified soil, especially when the IWC was greater than the optimum water content. The maximum strength increase rate could be up to 98.2%. However, at an IWC of 20.8%, the strength increase rate could still reach approximately 72%. Correlation analysis showed that the solidification mechanism of the hydrophobic polymer was mainly electrostatic interactions. Variable water contents mainly affected the formation of polymer bonding and thickness of DDL. The utilization of hydrophobic polymer for soil improvement in backfill projects shows great potential in light of these findings.