The invention discloses a nitrogen-substituted podophyllotoxin derivative with anti-tumor activity and a preparation method and use thereof. According to the method, 2-aminopyrimidine, 2-aminopyridine, 2-amino-3-methylpyridine, 2-amino-4-methylpyridine, 2-amino-5-methylpyridine, 2-amino-4,6-dimethyl pyridine, 3-aminopyridine, 3-amino-4-methylpyridine, 5-amino-2-methylpyridine, 3-amino-2-chloropyridine or 4-amino-2-chloropyridine is respectively introduced to an activated C-ring fourth position of a podophyllotoxin compound through nitrogen substitution reaction, so as to obtain the nitrogen-substituted podophyllotoxin derivative, represented by a formula (V) shown in the specification, with excellent anti-tumor activity. The nitrogen-substituted podophyllotoxin derivative disclosed by the invention acts on tumor cells through multiple ways and multiple target points, and the anti-tumor activity of the nitrogen-substituted podophyllotoxin derivative is remarkably improved compared with that of the podophyllotoxin compound. The compound disclosed by the invention can be used for preparing anti-tumor drugs and is clinically applied to anti-tumor treatment.