The recycling of tree nut shells biomass (TNSB), a million-tons level inedible food waste, toward food and drug applications should be one of the most promising valorization pathways. However, therein biggest opportunity and challenge is to fully dig for treasure such as its own high-value biomacromolecules and natural active ingredients. This study completed a food and drug grade extraction by using five TNSB sample (i.e., walnut shell, hazelnut shell, macadamia shell, pin nut shell, and pistachio shell), two green solvents (water and ethanol), and cleaner room temperature green extraction (RTGE) technology; and revealed the molecular basis of the raw materials and their extracts through systematic and in-depth molecular analysis. The results showed that TNSB have extremely high lignin content, and their extracts (whether water or ethanol) are rich in phenolic compounds, which results in the latters having extremely strong antioxidant activities (comparable to vitamin C) and α-amylase inhibitory activities (comparable to acarbose). More specifically, walnut shell has the highest ever lignin content of 57% in all reported biomass. The water extract of walnut shell has more excellent properties, such as 147.65 mg/g of total reducing sugars (TRS), 60.49% of total phenolic content (TPC), 0.24 mg/mL of IC50, DPPH, 0.08 mg/mL of IC50, ABTS, and 13.44% of α-amylase inhibitory activity. Further molecular information shows that these reducing sugars are glucose, fructose, arabinose and fucose, and these phenolic compounds include phenol, vanillin, vanillic acid, p-hydroxybenzoic acid, gentisic acid, gallic acid, protocatechuic acid, epicatechin, caffeic acid, and (trans)catechin. These results demonstrate fully that TNSB will become the preferred feedstock species for lignin-first biorefinery in the future, and walnut shell is undoubtedly the best one. Furthermore, TNSB-based RTGE extracts have the potential to be developed into natural antioxidants, preservatives, diabetes-therapeutic pharmaceutical preparations, nutraceutical and functional foods. In addition, we also used XLSTAT software to conduct a systematic attribution analysis, namely, principal component analysis (PCA) and agglomerative hierarchical clustering (AHC), revealing the inner relationship between the multifactors including TRS, TPC, DPPH, ABTS and α-amylase inhibitory activity among TNSB species.