A method for selective edge extraction in an optical scanning holography system is proposed based on annular pupil filters, in which a single two-dimensional optical scan is used to acquire the holographic information of a three-dimensional object based on the two-pupil heterodyne scanning technique. First, a small aperture filter and an annular pupil filter are used as two pupils to form a composite light field for scanning an object and extracting the edge information of an object. Then, the selective extraction of the anisotropy of an object is achieved by moving and destroying the symmetry of an annular pupil filter and simultaneously selecting two identical annular pupil filters. The computer simulation results show that the selective edge extraction of isotropy and anisotropy can be well achieved by using annular pupil filters in an optical scanning holography system.