According to the invention, early-flowering oil-used type variety 'YS-143' and late-flowering turnip variety 'VT-044' are taken as test materials, and the flowering time of the two in two conditions,namely long sunlight and short sunlight, are respectively observed. The cDNA sequence of the gene is cloned by taking two materials as a template simultaneously, and the amino acid sequence of the gene is analyzed by using a bioinformatics technology, so as to find the difference loci of the CCA1 genes of the early-flowering and late-flowering Chinese cabbage crops, and the difference loci is primarily confirmed by analysis such as bioinformatics and sequencing comparison, and then an InDel maker is developed. The nucleotide sequence of the InDel maker is ACCCTT, which is located on the sixthexon of the CCA1 gene of the early-flowering Chinese cabbage crop, but does not exist on the CCA1 gene coding region of the late-flowering Chinese cabbage crop. Finally, by verification, the InDel maker is taken as a functional marker for molecule assistant breeding operation. The molecular marker disclosed by the invention can be simply, conveniently and rapidly applied to breeding practice withhigh throughput.