Chang Zhensen, who was one of the chief physicians and famous veteran doctors of TCM in Shandong province, thought that it was hard to treat disease without learning about qi transformation or physiological function of zang-fu organs. He believed that kidney qi was the source of power for human body and flexibly used Jinkui Shenqi decoction in clinical treatment by superb. This paper summarized experiences of Chang Zhensen’s clinical application of Jinkui Shenqi Decoction on treating internal disease, gynecological disease and pediatric disease. It heightened the confidence on the application of classical prescription in traditional Chinese medicine.