Obesity is a complex metabolic disease, which has a certain relationship with intestinal microflora. To evaluate the effect of high protein diet from soybean protein and pork protein on obese mice and its intestinal microflora structure, a C57BL/6J obesity mice model was firstly induced by high fat diet. Then obese mice were randomly divided into 4 groups according to body weight, high fat diet (HF) group, normal recovery (NR) group, high soy protein diet (HSP) group and high pork protein diet (HPP) group, and dietary intervention was taken by obese mice for 12 weeks. Besides, the blank control (NC) group was set. The intervention effects of high protein diet from soybean protein and pork protein on obese mice were analyzed through inflammatory factors and adipose micro-structure measurement. Cecal contents were collected to analyze the differences of intestinal microflora between each group by 16S rRNA high-throughput sequencing technology. Compared with NR group, the body weight, lipopolysaccharides level and TNF-α mass concentration in serum of mice in HSP and HPP groups were decreased in different degree. Meanwhile, liver HE staining and oil red O staining showed that liver fat deposition was significantly reduced in HSP and HPP groups (P<0.05). High fat diet and high protein diet significantly reduced the species richness and evolutionary diversity of intestinal microflora including evolutionary relationships, but there was no significant difference in species diversity and evenness (P>0.05). The high protein diet improved the obesity of mice and changed the intestinal microflora structure of obese mice. The results aimed to provide a new understanding for the intervention and improvement of obesity by regulating intestinal microflora through dietary.