With the development of optical technology, optic-mechanical-electric technology becomes a trend. An integrated, arrayed and miniaturized optical system was required. Binary optical element is famous for its excellent performance in light-wave transformation. Double-layer binary optical element has high diffraction efficiency over wide wavelength range. However, in the fabrication of double layer BOE, many errors occurred, such as height error, periodic error, multi-mask fabrication error etc.A theoretical analysis of these errors was carried out based on scalar diffraction theory, and a MATLAB simulation was implemented. The simulation result indicated that the diffraction efficiency deteriorated if the height errors occurred in different direction rather than in the same direction. Therefore, height errors from different direction should be avoid in fabrication. If the multi-mask fabrication error is occurred from different direction, the diffraction efficiency will decrease more quickly than from the same direction, so multi-mask fabrication error from different direction should be avoid as much as possible. Compared to height error and multi-mask fabrication error, other four errors have varying degrees of impact on the diffraction efficiency.