Natural phenolic compounds are rich in cereal and pulse seeds and their dietary functions tend to improve dramatically during germination. This article reviews recent research on the transformation of phenolic compounds during seed germination. In particular, it highlights the classification of crude phenolic compounds that can be divided into extractable and non-extractable phenolic compounds based on the biosynthesis process and extraction method. It also recommends grouping resorcinol lipids in the category of extractable phenolic compounds as non-polar solvent extractable phenolic compounds. Moreover, it discusses the variation of the different form of phenolic compounds and proposes a possible metabolic model of these phenolic compounds for seeds germination. This article is crucial for phenolic compounds research, cereal and pulse seeds germination, and food ingredients industry.