Abstract: As a leading country in saline-alkali land distribution, China faces significant threats to its food security from soil salinization. Salt stress severely inhibits rice seed germination by inducing osmotic imbalance and ionic toxicity, presenting a major constraint for rice cultivation in these areas. Melatonin (MT), an indole derivative, has demonstrated efficacy in enhancing salt tolerance in various crops, primarily through reactive oxygen species (ROS) scavenging and ion homeostasis regulation. However, its specific regulatory mechanisms on internal water metabolism during the critical seed germination stage under salt stress remain poorly understood. The germination process is fundamentally driven by water uptake and redistribution, yet conventional methods lack the capability for real-time, non-destructive monitoring of internal water status and phase transitions. Low-field nuclear magnetic resonance (LF-NMR) and magnetic resonance imaging (MRI) techniques offer a powerful solution by enabling non-invasive detection of hydrogen proton signals, thereby precisely characterizing water content, migration, and phase distribution within biological tissues. This study investigated the regulatory effects of exogenous MT on germination characteristics and internal water dynamics in rice seeds under salt stress using the japonica conventional rice cultivar 'Tijin'. A preliminary NaCl concentration gradient screening established 150 mmol/L as the standard salt stress condition (N150 treatment), which reduced the germination potential to 32% of the water control. The experimental design included a water control group (CK1), a salt stress control group (CK2, N150), and five MT treatment groups (50, 100, 200, 400, and 800 μmol/L MT + N150). Germination physiological indices were monitored, and LF-NMR (utilizing CPMG sequence) combined with MRI (using MSE sequence) were employed to track internal water dynamics and phase changes throughout the 72-hour germination period. The results revealed a concentration-dependent biphasic regulation of rice seed germination by MT under salt stress. The 200 μmol/L MT concentration was identified as optimal, significantly enhancing germination rate (94.33%), germination potential (78.67%), fresh weight accumulation, and the growth of radicles, plumules, and secondary roots. This treatment effectively alleviated salt-induced osmotic stress and ionic toxicity, maintaining stable cell membrane permeability. MRI pseudo-color mapping vividly illustrated the dynamic internal water distribution, allowing the germination process to be delineated into three distinct stages based on physiological metabolism: imbibition (0-24 h), initiation (24-48 h), and germination (48-72 h). LF-NMR T₂ relaxation analysis characterized four water fractions: strongly bound water (T₂₀, 0.1-1 ms), bound water (T₂₁, 1-10 ms), semi-bound water (T₂₂, 10-100 ms), and free water (T₂₃, 100-1000 ms). Medium MT concentrations (200 and 400 μmol/L) effectively maintained water phase stability, exhibiting relaxation characteristics akin to the CK1 group. In contrast, the high MT concentration (800 μmol/L) failed to confer beneficial effects, with its water phase features, including a consistently reduced T₂₂ peak area, converging towards those of the salt-stressed CK2 group. In conclusion, an appropriate concentration of exogenous MT (200 μmol/L) can effectively mitigate the inhibitory effects of salt stress on rice seed germination. The integration of LF-NMR and MRI techniques provides a robust, non-destructive, and precise methodology for analyzing internal water dynamics and phase transitions. This study elucidates the patterns of internal water changes associated with MT-mediated alleviation of salt stress during rice seed germination, offering valuable theoretical insights and a technical reference for advancing research on rice seed salt tolerance and the development of related enhancement strategies.