The present invention discloses a preparation method and an application of cryptosporidium protein kinase 660 C-terminal protein. The preparation method comprises the following steps: S1, using amplification primers shown in SEQ ID NO:1-2 to conduct PCR amplification reaction to obtain a Cp 660 C gene segment; S2, carrying out double enzyme digestion on the Cp 660 C gene fragment and a prokaryoticexpression plasmid and conducting connection to obtain a Cp 660 C recombinant plasmid; S3, transferring the Cp 660 C recombinant plasmid into an expression host bacterium and picking a positive clonebacterium; S4, carrying out amplification culture on the positive clone bacterium until a growth logarithmic phase and carrying out induced expression; S5, carrying out refrigerated centrifugation onbacterial liquid after the induced expression, collecting bacterium body, discarding supernatant, washing the bacterium body, carrying out re-suspension, adding a protease inhibitor, carrying out icebath ultrasonic lysis on the bacterium body to obtain a lysate, then carrying out low-temperature centrifugation to obtain supernatant, and conducting filtering with a filter membrane; and S6, takingthe filtered supernatant in the step 5, purifying the supernatant through a Ni column, eluting the supernatant, and collecting a target protein. The method can obtain the recombinant protein with high purity and high antigen specificity, and the purified protein can be further used for analyzing and researching functionality of the cryptosporidium protein.