The consumption of raw yam tuber through grated yam “tororo” is a major and popular diet in Japan. However, few studies have been undertaken to evaluate the digestive characteristics of raw yam tubers. This study aimed to fill this gap by investigating the changes in the protein profile, protein and starch digestibility, antioxidant capacity and microstructure of two typical yam tubers (Nagaimo N-10 and Nebaristar) in the Japanese diet, applying a simulated in vitro digestion method. Results showed that both samples contained a considerable protein content of about 11% (dry basis) and a protein digestibility of 43–49%. The electrophoretic patterns confirmed that dioscorin was the main protein of the yam tuber, and it could be digested into peptides and free amino acids with low molecular weight during in vitro digestion. The starch hydrolysis results suggested that eating raw yam tuber cannot induce a fast glycemic increase for consumers due to a low starch digestibility of 4.4–6.1%. In addition, Nebaristar showed a higher bioaccessibility in some key amino acids and total phenolic content than the Nagaimo N-10. This study provides some essential nutritional information and simulated digestion behaviours of the raw yam tubers, which could be useful for consumers and industries when buying and processing yam tubers from the perspective of changes in the nutritional profile during digestion.