The hydrogen isotopes in liquid and frozen water samples were analyzed by laser ablation molecular isotopic spectrometry (LAMIS), which employs the molecular emission from laser-induced plasma for isotope analysis. Molecular emission bands of OH and NH radicals were observed, and their spectral features were characterized in accordance with sample matrix and measurement conditions. The OH and NH bands exhibit different emission behavior, which was attributed to formation kinetics and thermodynamic factors. Under optimized condition, isotopic shift between hydrogenated (OH and NH) and deuterated (OD and ND) species was measured at individual rotational branches. By using these molecular bands, the partial least squares regression (PLSR) structure was established for quantitative analysis of hydrogen isotope and evaluated by cross-validation in terms of accuracy and precision. The PLSR result was good with root mean square error of prediction (RMSEP) of 0.3–0.7% for all species. Particularly, the case using OH/OD emission from liquid water revealed the most accurate result with RMSEP of 0.33%. It was affected by the quality and reproducibility of spectral data determined by utilized species. This study not only supports the behavioral understanding of molecular radicals in laser-induced plasma, but also identifies the feasibility of LAMIS for real-time application to quantitative analysis in various sample matrices.