This comparative study to analyze the changes in physiological and biochemical in the same condition by unpolished coix seed of 5 varieties that have been produced in Guizhou or Laos, selecting out optimal germination of varieties, then optimizing the germination rate and germination by using γ-amino butyric acid(GABA) as evaluation index, using single factor experiment and orthogonal design methods, tracing its main nutrients and functional components dynamically. The results showed that the sprouts of GZ-1 from Guizhou had the highest germination rate, free amino acids and γ-amino butyric acid (GABA) levels among the five varieties. Based on the sprouting rate and GABA level, an optimal germination condition for variety GZ-1 was developed by using a single factor test followed by an orthogonal experiment design. Under the optimal condition of temperature 28 ℃, relative humidity 90%, and germinating time 96 h, Germination rate of 89%, the level of GABA increased to 78.18 mg/100 g. During germination, protein, starch and polysaccharides in the sprouts decreased while reducing sugars, free amino acids, GABA, and vitamin C, B1 and B2 increased gradually. However, the change of lipids level in sprouts was not significant. With higher level of bioavailable essential nutrients, the germinated unpolished coix seeds could be considered as a health promoting food material.