Understanding quantum tunneling principles over two-dimensional (2D) van der Waals (vdW) ferromagnets at the atomic level is essential and complementary to the fundamental study of low-dimensional strong correlated systems and is critical for the development of magnetic tunneling devices. Here, we demonstrate a local electric-field controlled negative differential conductance (NDC) in 2D vdW ferromagnet Fe3GeTe2 (FGT) by using scanning tunneling microscopy (STM). The STM reveals that NDC shows an atomic position dependence and can be precisely modulated by altering the tunneling junction. The band shift together with electric-field-driven 3d-orbital occupancy modulates the sensitive magnetic anisotropic energy (MAE) in 2D FGT and consequently leads to electric-field-tunable NDC, which is also verified by theoretical simulation. This work realizes the electric-field-driven NDC in 2D ferromagnet FGT, which paves a way to design and develop applications based on 2D vdW magnets.