Imbibition, embryonic peripheral tissue rupture and radicle emergence are generally considered as key development stages of germinating tobacco seed. However, the similarities and differences of metabolism among them are yet to be explored. Present study investigated the transcriptomes distinctions at various developmental stages in tobacco seed. The results showed that 2730 and 2708 transcripts were significantly up-regulated during imbibition and radicle emergence respectively, which were significantly higher than that of 1969 during endosperm rupture. Thirteen patterns of short time-series expression profiles (STEM) were found to be significantly clustered, including the patterns of three stages continuously up-regulated during imbibition, endosperm rupture and radicle emergence, any two or only one of up-regulated, but not patterns of continuously or any two stages of down-regulated, even one stage of down-regulated pattern clustered was just focused on the endosperm rupture. Of them, we focused on the continuously up-regulated pattern in this study and noticed 221 transcripts enriched in this pattern, which are participated in ABA signal pathway, cell wall hydrolysis, and light signal transduction metabolism. In addition, the methionine metabolism was stimulated after imbibition, cell division, growth and differentiation were significantly increased prior to endosperm rupture, and photosynthesis rise significantly in radicle emerged seeds. This study preliminarily revealed the metabolic differences among four developmental stages during seed germination in tobacco.