The invention relates to a nutritional and safe soy milk making method of a soy milk maker, and aims at the problems that for a traditional view, water for soaking soybeans is not suitable for soy milk preparation, and dissolving-out condition of a functional component during soy milk making is almost ignored in the prior art. A main functional component soy isoflavone in soybeans plays an important role in the aspects of prevention and treatment for breast cancer and prostate cancer, improvement of climacteric syndrome and osteoporosis, protection for a cardiovascular system and the like. In order to change the misconception and obtain higher-content and high-activity isoflavone soybean milk to improve nutritive values of the soy milk, the soybeans are heated, sterilized and soaked for a long time before soy milk making, after the soybeans are soaked with the method, malignant bacteria in water can be effectively killed, and water for soaking the soybeans can be used for soy milk making; and besides, the activity of beta glucosaccharase in the soybeans can be maintained, glucosidic isoflavone hard to be absorbed by a human body is hydrolyzed into aglycone isoflavone, so that isoflavone in the soybeans are sufficiently released, and a better healthcare effect can be provided for consumers.