The invention relates to a method of developing SNP (single nucleotide polymorphism)-SSR (simple sequence repeat) molecular makers closely linked with SNP by utilizing SNP. The method comprises the following steps of: (1) finding according to a position of a known SNP molecule of a to-be-developed sample on a genetic map to obtain an SNP marker extending sequence; (2) comparing the SNP marker extending sequence in a genome sequencing database of the to-be-developed sample, and selecting a sequence segment; (3) feeding complete type, incomplete type and composite type SSR to obtain SSR locus based on repetitive sequence length not less than 20bp; (4 designing primers according to flanking regions of SSR lotus, selecting the primers with stable and clear banding patterns through PCR (polymerase chain reaction) amplification and sequencing to obtain a to-be-verified molecular marker; and (5) preparing the SNP-SSR molecular marker by utilizing the primer of the to-be-verified molecular marker. The method disclosed by the invention can quickly and greatly screen out SNP-SSR molecular markers closely linked with the SNP.