Objective The biological basis of phlegm and blood stasis related syndromes was explained by exploring the SNPs of glucose and lipid metabolism related genes in patients with fatty liver in Kunming, and the correlation between ZJU related indexes and the syndromes of phlegm and blood stasis. According to this research, it provides the basis for the objectification of syndrome differentiation. Methods Forty cases of FLD were divided into phlegm and blood stasis syndrome as experimental groups, forty cases healthy people as the control group. Height, weight, liver function, FPG, TG, liver B-mode ultrasonography, SNPs of sugar and lipid metabolism related genes were tested. Results The ZJU index in this research showed that there was a significant difference between FLD group(37.82 ± 4.97) and contrast(33.26 ± 2.83)(P<0.01). As the SNPs of sugar and lipid metabolism related genes were detected, the difference between LEPR rs1137100（K109R） and PNPLA3 rs738409（I148M） was found. But there was not directly correlation between genotypes and occurrence of FLD. Conclusion Difference in SNPs of LEPR rs1137100（K109R） and PNPLA3 rs738409（I148M） may play an important role in the aggravation of phlegm-stasis related syndromes. The two genes may be one of the biological bases of phlegm-stasis related syndromes.