This study was aimed to detect the relationship between protein inherent molecular structure features and protein rumen degradation kinetics and intestinal digestibility of 3 types of co-products from bio-oil processing including rapeseed meal, canola meal and soybean meal for dairy cattle. Three sources of rapeseed meal, 3 sources of soybean meal and 3 sources of canola meal were collected in 2014. The protein molecular structure in terms of chemical functional groups in these feed samples was analyzed using attenuated total reflectance-Fourier transform infrared spectroscopy (ATR-FT/IR) instrument. Rumen protein degradation kinetics was determined using in situ nylon bag method. Intestinal digestibility of rumen undegraded feed protein were determined according to the 3-step in vitro procedure with 12h pre-rumen incubated feed samples. The PROC MIXED procedure of SAS 9.3 was used to analyze the univariate protein spectral data, protein degradation kinetics and intestinal digestibility data. After normality test of the data, PROC CORR of SAS with a SPEARMAN option was used to investigate the relationship between protein molecular structure and metabolic characteristics in dairy cattle. Significances were declared at P < 0.05. The results showed that the ratio of protein amide I to amide II spectral peak height had a highly negative correlation with rumen undegraded protein (RUP^NRC; r = −0.67, P = 0.05), intestinal absorbable rumen degraded protein (IADP; r = −0.67, P = 0.05), intestinal digestible protein (IDP; r = −0.77, P < 0.05) and total digestible protein (TDP; r = −0.67, P = 0.05). Additionally, the ratio of protein secondary structure α-helix to β-sheet height was negatively correlated with rumen undegradable protein (RUP^NRC; r = −0.67, P < 0.05), rumen degradable protein (EDCP; r = −0.83, P < 0.05), and total digestible protein (TDP; r = −0.93, P < 0.05). The results indicated that protein molecular structure was highly related with its nutrient supply to dairy cattle.