The primary objective of this study was to develop a model to predict Cornell Net Carbohydrate Protein System (CNCPS) protein degradation and digestion based on protein molecular structure changes induced by bio-energy processing in different types of co-products (CoPR, CoPC, CoPS = co-products from bioprocessing of rapeseed, canola seed, and soybean, respectively). The results showed that the inherent structure changes induced by the processing had a close relationship with CNCPS predicted protein degradable, undegradable, and digestible contents. The amide I to II ratio and α-helix to β-sheet ratio could be used to predict total degradable protein (R(2) = 0.99, RSD = 0.84, P < 0.001). Total CNCPS intestinal digestible protein could be predicted by protein structure α-helix to β-sheet ratio (R(2) = 0.93, RSD = 0.33, P < 0.001). In conclusion, the processing-induced protein molecular structure changes were highly linked to protein nutritive value of the co-products and could be used as predictors for CNCPS protein degradation and digestion in dairy cattle.