Most of tumor antigens are self-proteins with poor antigenicity because of immune tolerance. Here, we describe DNA shuffling for overcoming the tolerance of tumor antigens such as vascular endothelial growth factor (VEGF), a growth factor associated with tumor angiogenesis. VEGF genes from mouse, rat, human, and chicken were randomly assembled to chimeric genes by DNA shuffling for constructing an expression library, then screened by PCR, SDS-PAGE, and immunization. A chimeric protein named as No. 46 was selected from the library with the strongest immunotherapy effects on mouse H22 hepatocellular carcinoma, which could induce long-lasted and high level of antibodies recognizing VEGF in mice. Immunization with this chimeric protein could significantly inhibit tumor angiogenesis, slow down tumor growth, increase the survival rate of tumor-bearing mice, and inhibit the lung metastases of tumor in mouse. Treatment with the anti-VEGF IgG induced by this chimeric protein also significantly inhibited tumor growth and improved the survival rate of tumor-bearing mice, by blocking the tyrosine phosphorylation of ERK1/2 pathway of VEGF-VEGFR interaction. Our study provides an efficient approach to overcome the immune tolerance of self-antigens for developing novel tumor vaccines.