Concrete is vulnerable to water and chloride ingress because of its porous structure and hydrophilic hydration products. To address the poor dispersion, hydration interference, and strength loss often associated with conventional hydrophobic modifiers, this study synthesized a nano-silicon hybrid hydrophobic polymer ester (HPE) based on C12 alkyl carboxylate groups. Unlike conventional nano-silicon or alkyl-based modifiers that mainly rely on pore refinement or surface hydrophobization alone, HPE integrates C12 alkyl carboxylate groups with nano-silicon to construct multiple transport barriers. The effects of HPE dosage on concrete properties and transport-inhibition mechanisms were evaluated using contact angle, water absorption, electrical flux, rapid chloride migration, natural chloride diffusion, compressive strength, SEM, and MIP tests. HPE increased the contact angle from 14° to 78° and reduced long-term water absorption to 28% of the control. The electrical flux and chloride migration coefficient decreased to 48% and 62% of the control, respectively. MIP results showed reductions of 67.9% in the most probable pore diameter and 28.4% in total porosity. The enhanced durability is attributed to hydrophobic film formation, in-situ pore-blocking particles, and nano-silicon-assisted pore densification.