Lignin-carbohydrate complexes (LCCs) have recently emerged as natural products with pharmaceutical and nutraceutical potential. Here, we compared the structure of LCCs from ginkgo (GK, gymnosperms), wheat straw (WST, monocotyledons), and aspen white poplar (AW, dicotyledons). We also investigated the biotransformation of LCCs by intestinal microbiota in vitro. We found that human intestinal microbiota could use LCCs as a carbon source for growth, breaking resistant cross-linkages in LCCs to generate a plethora of short-chain fatty acids (SCFAs) and aromatic compounds with putative beneficial effects on human health. The yield of SCFAs reached 1837.8 ± 44.1 μmol/g using AW LCCs as a carbon source. The biomass of intestinal microbiota increased the fastest using GK LCCs. The greatest amounts of phenolics were present at 4 h in a WST LCCs fermentation system. Many phenolic acids with potential bioactivity were obtained after 24 h fermentation using each LCCs, such as ferulic acid.