The surfaces of diffraction optical element (DOE) are often deep and discontinuous, which lead to some difficulties for measurement of the 3-D surface topography of DOE. The generalized two-wavelength interferometry and a new data processing method are proposed, which effectively overcome the difficulties. Based on these techniques, a new measuring system has been set up with existing conditions. The system′s longitudinal resolution is 0.5 nm, the transversal resolution about 0.5 μm(NA=0.4), the measuring accuracy within the whole longitudinal measuring range is better than 1.3 nm.