The three-dimensional (3D) culture model of neuroendocrine tumor H727 cells was established by using the agarose gel as culture matrix, which provided a new method for drug screening of neuroendocrine tumors. As VEGFR inhibitor, sunitinib and axitinib were applied to inhibit human neuroendocrine H727 cell line in two-dimensional (2D) and 3D culture models. The inhibitory rate of H727 cells with different drug concentration were assessed by CCK-8 assay method and combined with using the FDA/PI double staining and the digital microscope analysis system. When the concentration of sunitinib ≥4.0 μmol/L, the H727 spheroids began to split, and the apoptosis of H727 cells occurred, the sizes of multicellular spheroids was significantly reduced in the groups of high-dose axitinib. These results illustrated that sunitinib and axitinib can effectively inhibit the growth and proliferation of neuroendocrine tumor H727 cells. Sunitinib and axitinib can also promote apoptosis of H727 cells.