Glycine betaine (GB), a naturally occurring osmolyte, has many biological functions and is used in food supplements, pharmaceuticals, and animal feed. GB usually exists as a zwitterion in aqueous solutions. Due to the hygroscopic property of GB, protonated form of GB, GBH+ (noted as GBH) is often used. In order to understand the hydration structures of GB and GBH at the atomic and electronic-structure level, a combination of ab initio molecular dynamics simulations and electronic structure calculations based on density functional theory (DFT), single-excitation configuration interaction method, and coupled-cluster ansatz was utilized. A hybrid explicit–implicit solvation model was used to elucidate solvent effects. Within the hybrid scheme, microsolvated structures of GB and GBH with up to 100 water molecules were obtained, showing that water molecules bind to GB and GBH in a dramatically different manner. By calculating the molecular electron-density distributions at PBE0-D4/def2-TZVP level, it shows that the variation of electron density for GB is more significant than GBH, suggesting that GB can interact with more water molecules than GBH. The interaction energies of GB–(H2O)n and GBH–(H2O)n systems (n = 1–6) at DLPNO-CCSD(T)/cc-pVQZ level highlight the difference from an energy point of view. Using the microsolvated structures of GB and GBH, the features of experimental K-edge spectra can be reproduced using the efficient PNO-ROCIS/B3LYP method, implying the reliability of the hybrid explicit–implicit solvation approach. The results suggest that complementary insights into the geometries and electronic structures of GB and GBH could be obtained through combined methods, which provides a methodological approach for understanding the hydration structures of zwitterionic and charged molecules.