This study was carried out to find material basis of which effect germination rate of Salvia miltiorrhiza Bge seeds in different years and in different areas. The results can be used in quality identification and advising storage conditions. Routine method were used to study the basic qualities, such as physical purity, weight of 100 seeds, seed moisture and germination. GC-MS were used to detect fatty acids and UV spectrophotometer was used to detect reducing sugar. The germination and viability of new seeds were much higher than that of aged. Weight of 100 seeds, seed moisture, fatty acids of same origin new seeds were higher than that of aged. However there was no correlation between different areas. Content of reducing sugar of same origin new seeds were higher than that of aged, also there were no correlation between different areas. Unsaturated fatty acids content of the new seeds was 80.90% which was much higher than that of aged. Linoleic acid was the main Unsaturated fatty acids. Saturated fatty acid content was 19.10% which was much lower than that of aged. Palmitic acid was the main saturated fatty acids. Data showed that unsaturated acids were auto oxidized to saturated acids in the process of storage. Germination rate was decreased as storage time prolonged.