The objectives of this study were to reveal the effects of heating method and variety on (1) protein molecular structure spectral features revealed by Attenuated Total Reflectance-Fourier transform infrared spectroscopy (ATR-FTIR), and (2) ruminant relevant protein chemical profiles, protein subfractions, rumen degradable protein (RDP), rumen undegradable protein (RUP), and intestinal protein digestibility using the Cornell Net Carbohydrate and Protein System (CNCPS) in oat varieties [CDC Nasser (feed-type oat) and CDC Seabiscuit (milling-type oat)]. Heating method included control (raw), dry heating (DH), moist heating (autoclaving, MH), and microwave irradiation (MIR). The dry matter (DM), crude protein (CP), and neutral detergent fiber (NDF) contents in CDC Nasser were 934, 107, and 252 g/kg DM, respectively; the contents of these nutrients in CDC Seabiscuit were 933, 110, and 268 g/kg DM, respectively. Heat processing significantly affected the total RDP (TRDP, P < 0.001), which was higher for DH than MIR and MH in CDC Nasser (5.46%, 5.01%, and 4.45%DM). Conversely, MIR had a higher value for TRDP than DH and MH in CDC Seabiscuit (5.32%, 5.24%, and 4.51%DM). The total RUP (TRUP) was higher for MH than MIR and DH in both varieties (P < 0.001). The intestinal digestible feed protein was similar between the varieties (P = 0.308); however, DH and MH reduced the value, while MIR increased it compared to the control (P = 0.010) for both varieties. The results from the ATR-FTIR analysis showed an interaction between varieties and heat processing in the protein secondary structures α-helix (P = 0.003), β-sheet (P = 0.031), and their ratio (P = 0.030). Moreover, in the multivariate analyses, no independent groups were observed between the raw and the three heat processing methods in the protein-related molecular structure of oats. In conclusion, heat processing altered the protein subfractions, the TRDP, and TRUP, affecting intestinal protein digestibility. The ATR-FTIR spectroscopy with univariate molecular analysis showed heat processing-induced molecular structure changes in the protein-related spectral profiles in CDC Nasser and CDC Seabiscuit.