A preparation method of a novel natural bioactive peptide Tubulysin U includes: dissolving a compound 2 in trifluoroacetic acid, heating under reflux to prepare an intermediate, reacting with a compound 3 and N,N-diisopropylethylamine to obtain a product, reacting the product with 2, 6-dimethylpyridine and tert-butyldimethylsilyl trifluoromethanesulfonate, adding sodium hydroxide after the reaction to prepare an intermediate acid, reacting the intermediate acid with a compound 6, HATU and N,N-diisopropylethylamine to obtain a product, adding triphenylphosphine to prepare an intermediate amine, adding a compound 8 and HATU to react, adding ammonium fluoride to prepare a first intermediate, adding sodium hydroxide to the first intermediate to prepare a second intermediate, adding acetic anhydride to the second intermediate to prepare a third intermediate, adding trifluoroacetic acid to the third intermediate to prepare a fourth intermediate, and adding formaldehyde and sodium cyanoborohydride to the fourth intermediate to react, thereby obtaining a target product.