Germination is an effective and sustainable processing method in enhancing nutrition quality of cereals. In order to improve the nutritional value of naked oat, the effect of germination time on oat quality was investigated in this study. The results showed that germination didn't have effect on protein content. However, germination could activate endogenous lipase and amylase, which led to the decrease of lipid content and the changes of the micromorphology. The contents of free amino acids decreased first and then increased with the extension of germination time. Additionally, germination changed the amino acid components of the oat, resulting in the decreases of glutamic acid and serine, and the increases of alanine, methionine and leucine. Gastrointestinal simulation in vitro showed that germination could change the digestion properties of oat starch, protein and lipid. Compared with the 0-day germinated oat, the releasing content of reducing sugar declined as 17.95 mg/g lower, the degree of protein hydrolysis increased as 14.23%, and the releasing content of fatty acid was 29.73 μmol/g lower than the 1-day germinated oat, respectively. Based on the results above, we found that 1-day germinated oat had the advancements of lower GI value and lipid digestion and higher protein digestion, and our study could provide proper methods in promoting the processing and utilization of naked oats.