The purpose of this study is to identify the QTL associating with low temperature germination（LTG）in rice and screen germplasm resources showing strong cold tolerance during germination, laying a foundation for cold-tolerant germination-related molecular marker-assisted breeding. Fifty-seven rice varieties with strong cold tolerance during germination were obtained by counting the LTG rate of 309 rice core germplasm resources from Guangdong province, China. Using the LTG rate in conjugation with high-density SNP markers, eleven QTL were identified by genome-wide association scanning (GWAS), of which qLTG2-1, qLTG7-1, qLTG7-2 and qLTG10-1 were resided with previously-identified QTL. qLTG11-1, as the most significant newly-identified QTL, was subjected for RNA-seq and qRT-PCR, in order to predict its candidate genes. LOC_Os11g07020, which is found surrounding qLTG11-1, showed different expression patterns in varieties with high and low germination rates during LTG. This gene encodes for a fructose-1,6-bisphosphate aldolase isozyme, which may regulate glycolysis reaction to affect cold tolerance during germination. Collectively, this study identied 57 rice varieties with strong cold tolerance during germination as well as 11 QTL for LTG, which laid a theoretical foundation for molecular marker-assisted breeding of cold tolerance at germination stage.