The invention belongs to the field of genetic engineering and reproductive medicine and discloses a low frequency SNV marker associated with sporadic non-syndromic CHD (congenital heart disease) auxiliary diagnosis and an application of the low frequency SNV marker. The marker is a combination of 41 low frequency SNVs such as rs75423398, rs7527798, rs200531164, rs6756629, rs139026854, rs79043251, rs1801212, rs4956145, rs7689099, rs145248317, rs34525648, rs16891235, rs13194053, rs41269281, rs41270593, rs3130250 and rs3130379. The marker can be used for preparing a sporadic non-syndromic CHD auxiliary diagnosis kit.