The invention discloses a preparation method and application of a dual-targeting DNA nano drug-loaded complex. DNA single chains S1, S2, S4, S5, S7 and S8, a nucleic acid aptamer 1, a natural nucleic acid aptamer AS1411 and chemically modified nucleic acid four ligands AS1411-1, AS1411-2 and AS1411-3 are mixed in a TM buffer solution, the mixture is placed in a PCR instrument to be constructed, and a DNA tetrahedral Aptamer 1-AS1411, a DNA tetrahedral Aptamer 1-AS1411-1, a DNA tetrahedral Aptamer 1-AS1411-2 and a DNA tetrahedral Aptamer 1-AS1411-3 are obtained through construction respectively. According to the preparation method and application of the dual-targeting DNA nano drug-loaded complex, four dual-targeting DNA nano drug-loading systems based on CD44 and nucleolin nucleic acid aptamers are constructed, and compared with a single-targeting drug-loading complex and a negative control group, four dual-targeting drug-loaded complexes have stronger nuclease degradation resistance, capability of targeting melanoma A375 cells, capability of inhibiting proliferation of the A375 cells and capability of inducing the A375 cells to generate G1 phase retardation.