This study presents a novel strategy to simultaneously mitigate the early-age shrinkage and achieve hydrophobization of metakaolin-based geopolymer (MKG) pastes through the incorporation of organic admixtures including polydimethylsiloxane (PDMS) and sodium methylsilicate (SMS). The pore structure, wettability, moisture/water adsorption capacity, and internal moisture distribution are investigated through different techniques including MIP and LF-NMR. Results indicate that the autogenous shrinkage of MKG paste is reduced by 91.2 % and 41.6 % when adding 5 % PDMS and replacing with 20 % SMS, and the water contact angle increases to approximately 130° and 140°, respectively. The addition of organic admixtures significantly reduces the moisture adsorption and surface tension of the MKG matrix, and thus internal water tends to be transported into larger pores, leading to less liquid-vapor meniscus and lower capillary stress. Moreover, an underlying mechanism is proposed to explain the shrinkage mitigation of hydrophobized MKG paste, accounting for the moisture transfer tendency and internal stress distribution.