Objective: To explore ethnic distribution characteristics of SNPs associated with micronutrient deficiency risk of Chinese primary and middle school students, and to provide a basic reference for evaluating the risk of lack in micronutrient. Methods: Totally 143 SNPs reported in previous studies were collected, and DNA was exacted by using magnetic beads in frozen blood cell samples from the 2016 nutrition health survey project of 1 130 primary and middle school students, competitive allele method was used to detect SNP genotyping. GO significant enrichment analysis R software package to PCA, kinship and linkage disequilibrium analysis were used for analysis of features of candidate SNPs. If there was a population structure, the FaST-LMM model was used for correlation analysis. Results: The GO significant enrichment results showed that differentially expressed genes were mainly enriched in the biological process grouping, including catalytic activity, transport activity, energy metabolism pathway, steroid hormone, coenzyme, biological processes of vitamin A, D and metabolism of water-soluble vitamins, involving transcription, translation and energy metabolism related genes. The results of 143 SNPs showed statistically significant differences in ethnic distribution, and SNPs on chromosome 3 presented significant differences among ethnic groups. Principal component analysis 1 showed that rs1799852 on TF gene had 25%-50% explanatory validity, rs2118981 on RBP2 gene and rs1830084 on SRPRB gene had 50%-75% explanatory validity, rs1358024, rs1525892, rs1880669, rs3811647, rs3811658, rs6794945, rs7638018 and rs8177248 on TF gene had more than 75% explanatory validity. Conclusion SNPs associated with micronutrient deficiency risk of Chinese primary and middle school students are characterized with ethnic distributions.