The aim of this study is to investigate the feasibility of applying super-hydrophobic slag (s-slag) to reduce the autogenous shrinkage and enhance resistance to carbonation of alkali-activated slag (AAS). The s-slag is produced by milling slag with stearic acid. The influence of the s-slag on the wetting behaviour is characterized by the water contact angle. It was found that the addition of s-slag has a significant influence on the hygroscopic and water absorption properties of the AAS. The hydration kinetics, reaction products, internal humidity, surface tension of pore solution and carbonation depth are investigated in order to explain the mitigation mechanism of the autogenous shrinkage and carbonation test. After applying 20% s-slag, the autogenous shrinkage and carbonation depth of AAS can be reduced by 68% and 70%, respectively compared to the reference. The surface coating by stearic acid reduces the contact between the slag and the activated solution, which decreases the heat release of AAS. The hydrophobic modification alters the wetting property of the AAS which is helpful to decrease the capillary pressure and obstruct contact with CO2. As a result, the autogenous shrinkage and carbonation depth are dramatically decreased. In addition, the introduction of the s-slag increases the compressive strength and flexural strength of AAS.