Lignin and lignin-carbohydrate complexes are important polymers for lignocellulosic biorefinery and functional materials, but those in ginkgo shells are not effectively analyzed and exploited. Based on this background, milled wood lignins (MWL_ML and MWL_FZ) and lignin-carbohydrate complexes (LCC_ML and LCC_FZ) were isolated from the shells of Ginkgo biloba L. cv. Damaling (ML) and Ginkgo biloba L. cv. Dafozhi (FZ) correspondingly, and were structurally characterized by comprehensive NMR spectroscopy. The results showed that ginkgo shells exhibited higher lignin (42%) and xylan (20%) content than general softwood species. Isolated MWLs were rich in guaiacyl units with the presence of ferulates and p-coumarates, and the molecular formula was C₉H_7.93O_2.73(OCH₃)_0.81 and C₉H_7.87O_2.76(OCH₃)_0.88 for MWL_ML and MWL_FZ, respectively. Phenolic hydroxyl of MWL_ML (1.38 mmol/g) and MWL_FZ (1.23 mmol/g) in ginkgo shells was much less than that in general softwoods, suggesting a higher etherification and condensation degree of ginkgo shells lignin, and β-5′, α-O-4′, and 4-O-5′ bonds were the main condensed structures. O-acetylated β-d-xylopyranoside and β-d-mannopyranoside were the main polysaccharides associated with lignin, and the acetyl groups frequently acylate the C₂ and C₃ positions. LCC_ML had more phenyl glycoside (0.035/Ar) and less γ-ester (0.026/Ar) linkages than LCC_FZ.