Objective　To identify genes associated with intravenous immunoglobulin (IVIG) resistance in Kawasaki disease (KD) through targeted enrichment technology, and to screen the high-risk population of KD. Method A total of 190 KD patients (33 IVIG non-responders and 151 IVIG responders) admitted from December 2016 to October 2018 and 99 healthy check-up children were selected. The genomic DNA of peripheral venous blood from the patients was collected, and the gene differences between the two groups were analyzed and compared by targeting capture and sequencing technology. Result There were significant differences in genotypes of FCGR3A (rs77144485), IL15RA (rs2228059) and IL6 (rs13306435) between KD children and healthy children (all P<0.05). There were significant differences in genotype frequencies of 10 single nucleotide polymorphisms (SNPs) loci in IL-2RB, IL-24, BMPR1A, GZMB, KDR, KIR2DS4, CARD11 and CHUK between IVIG resistant group and IVIG responsive group (all P<0.05). Conclusion　IL-2RB, IL-24, BMPR1A, GZMB, KDR, KIR2DS4, CARD11, CHUK were found to be significantly different in IVIG resistant group and IVIG responsive group by targeted enrichment technology.