The invention relates to a targeting CLL-1 embedded antigen receptor and application thereof. Particularly, the invention provides a polynucleotide sequence which is selected from (1) polynucleotide sequences including an encoding sequence of an anti-CLL-1 single chain antibody, an encoding sequence of a human CD8 hinge region, an encoding sequence of a human CD8 transmembrane region, an encodingsequence of a human 41BB intracellular region, an encoding sequence of a human CD3 zeta intracellular region, and an encoding sequence having segments containing an extracellular domain III and an extracellular domain IV of optionally-selected EGFR (Epidermal Growth Factor Receptor), wherein the encoding sequence of the anti-CLL-1 single chain antibody, the encoding sequence of the human CD8 hingeregion, the encoding sequence of the human CD8 transmembrane region, the encoding sequence of the human 41BB intracellular region, the encoding sequence of the human CD3 zeta intracellular region, and the encoding sequence having segments containing the extracellular domain III and the extracellular domain IV of optionally-selected EGFR are sequentially connected with each other; (2) a complementary sequence of the polynucleotide sequences. The invention also provides related fusion proteins and carriers containing the encoding sequences as well as application of the fusion proteins, the encoding sequences and the carriers. CLL-1-BBz-tEGFR CAR-T cells prepared by the targeting CLL-1 embedded antigen receptor disclosed by the invention have strong killing functions on specific tumor cells,CD107 alpha expression and IFN gamma secretion are higher, and the killing efficiency of the target cells is more than about 70 percent under the situation that an efficiency target ratio is 5 to 1.