Germination of Styrax japonicus seeds is promoted by warm stratification (WS) at $18-20^{circ}C$ followed by cold stratification (CS) at $4-5^{circ}C$. The objective of this work was to analyze the state and mobility of water molecules measured by $^1H$-NMR and endogenous gibberellins (GAs) and abscisic acid (ABA) by ultra performance liquid chromatography/mass spectrometry/mass spectrometry (UPLC-MS/MS) as influenced by WS and CS treatments had not previously been investigated. Styrax seeds that received 35 days of WS (35D WS) followed by 63 days of CS (63D CS) (35D WS+63D CS) germinated. Seeds that received only 35D WS failed to germinate. Endogenous $GA_1$, $GA_8$, $GA_{19}$, $GA_{20}$, and $GA_{53}$ were identified as well as $GA_{17}$, $GA_{23}$, $GA_{28}$, $GA_{29}$, and $GA_{97}$ by gas chromatography/MS (GC/MS) and UPLC-MS/MS in seeds that were treated with warm and cold stratification (WS + CS). This suggests that the early C-13 hydroxylation pathway [$-GA_{53}-(GA_{44})-GA_{19}-GA_{20}-GA_1-GA_8$] of GAs is a major biosynthetic pathway in the seeds. The concentration of $GA_{53}$ and $GA_{19}$ increased following WS and that of $GA_{53}$ increased after WS+CS. The concentration of $GA_{19}$ increased only slightly after WS+CS. The concentration of $GA_1$ increased only after WS+CS. ABA concentration significantly decreased following the WS treatment. It is concluded that the mobility of water molecules and water content in cotyledons and endosperm is increased following WS+CS treatments. The occurrence of C-13 hydroxylated GAs suggests that the early C-13 hydroxylation pathway, ${ ightarrow}GA_{53}{ ightarrow}GA_{44}{ ightarrow}GA_{19}{ ightarrow}GA_{20}{ ightarrow}GA_1{ ightarrow}GA_8$, is a major biosynthetic pathway in Styrax seeds.