Superhydrophobic surfaces applying on concrete can greatly improve the durability of concrete by preventing the damage from water. However, traditional design of superhydrophobic concrete surfaces by external coating encounters to problems of flaking and poor surface robustness, while that by adding hydrophobic agents or particles faces the challenges of strength damage of concrete. Drawing inspiration from the carbonation phenomenon of concrete, here a new design of in situ growing superhydrophobic structures on concrete is proposed: The concrete sample is impregnated into Mg2+-containing silane–water system with continuous CO2 injection. The contact angle of the concrete surface achieves 171.9° without obvious strength decrease after 120 min, which are mainly attributed to the formation of CaxMg1−xCO3 crystals with micro-nano-structures and the reduction of carbonates surface energy by silane. This superhydrophobic concrete structure can be divided into a superhydrophobic–hydrophobic–hydrophilic three layers structure, providing the stable water-proof protection under mechanical fatigue, capillary water absorption, UV aging, sulfate attack, and impurity water impact tests due to the in situ growing robust superhydrophobic structures. Furthermore, it captures 29.80 g m−2 CO2 during the reaction process, providing new insights for the design and preparation of eco-friendly superhydrophobic concrete.