Abstract: Based on the quaternion vector mathematical model \overrightarrow z = a + b\overrightarrow i + c\overrightarrow j + d\overrightarrow k , this paper determines that the corresponding relationship in structure is \overrightarrow z (human body vector)=a (body scalar)+b\overrightarrow i (gut flora vector)+c\overrightarrow j (mitochondria vector)+d\overrightarrow k (human brain vector) and the corresponding relationship in function is \overrightarrow z (holistic human)=a (human body for moving)+b\overrightarrow i (gut flora for eating)+c\overrightarrow j (mitochondria for breathing)+d\overrightarrow k (human brain for thinking). As a result, a new understanding of human structure and function is obtained, which means the "human body" is regarded as a combination of one scalar and three vectors. Thus, it embodies the logic of "creating bacteria first, then mitochondria, and man later" in the process of "human origin" in nature.According to above concepts, we can reasonably explain viewpoints and problems such as "chronic disease originating from the intestine", "hunger sensation coming from gut flora" and "eating five kinds of grains leading to hundreds of diseases", and can also promote the origin of chronic diseases from the previous "human gene pathogenicity" to a new understanding that "the pathogenic genes of intestinal flora come first and human genes come second", there by providing new ideas for chronic disease prevention and health management. The model also supports the traditional understanding of "harmony" rather than "confrontation" between man and symbiotic microorganisms, and provides a reference basis for a correct understanding of "man and nature" as well as "physical and mental health".