The coupled wave equations for second harmonic generation of flat-topped beams propagating in birefringent uniaxial anisotropic medium were presented. Specific physical models of single and twin BBO were established and numerical computation was carried out. The influences of beam waist, medium structure on second harmonic generation were analyzed. The calculation results indicate that a wider waist can make a better phase matching, so the second harmonic beam will maintain the flat-topped property better but with a lower intensity and twin crystal can eliminate beam walk-off in some way.