Selenium (Se) is an essential component of critical enzymes and is intricately linked to human health. Shiitake mushrooms (Lentinula edodes) are considered as good dietary supplements for producing Se-enriched foods due to their high protein content and ability to absorb minerals from growth substrates. In this study, the distribution of soluble Se in Se-enriched L. edodes was analyzed by microwave digestion and hydride generation-atomic fluorescence spectrometry (HG-AFS). In order to evaluate the absorption and conversion effect of Se by L. edodes, the Se-containing compounds in selenized L. edodes were quantitatively and qualitatively analyzed by high-performance liquid chromatography-electrospray ionization tandem mass spectrometry (HPLC-ESI-MS). It can be shown that L. edodes possessed a good biological transformation ability of organic Se enrichment though the quantitative analysis of three seleno-amino acids, selenocystine (Se-Cys2), methylselenocysteine (Se-MeSeCys) and selenomethionine (Se-Met), in selenized L. edodes. The structures of three unknown Se-containing compounds were identified by qualitative analysis, the results indicated that the possible structures were selenomethylmethionine (C6H14NO2Se), N-Acetyl-selenomethionine (C7H13NO3Se) and Se-methyl-5-selenoadenosinese-oxide (C12H18N5O3Se). The discovery of these Se compounds filled the research gap and provided a theoretical basis for molecular structure identification and mechanism study of organic Se in Se-enriched L. edodes.