Water bamboo shoots (WBS) are popular hydrophytic plant in China with a high nutritive value. However, WBS is susceptible to postharvest lignification. The firmness, lignin content, lignin composition, activity of lignin biosynthesis-related enzymes, and expression of lignin biosynthesis-related genes in WBS were determined after postharvest storage at 20 °C or 2 °C for 15 d or 63 d, respectively. The results indicated that lignin present in WBS was composed of G (vanillin and vanillic acid), H (p-hydroxybenzaldehyde and p-hydroxybenzoic acid), and S (syringaldehyde and syringic acid) monomers. During storage, the activities of phenylalanine ammonia-lyase, cinnamyl alcohol dehydrogenase, and peroxidase also increased. Moreover, the upregulated gene expression levels of lignin biosynthesis-related enzymes positively correlated with increasing lignin content, which were the key contributors to the lignification of WBS during storage. We observed that low temperatures delayed lignification by repressing the expression of lignification-related genes and suppressing the activity of lignin biosynthesis-related enzymes.