A-site substitution effects on the magnetic and lattice structure have been investigated for bilayer manganites, (La1-zNdz)(1.2)(Sr1-yCay)(1.8)Mn2O7, without changing the e(g)-electron concentration (x = 0.4). The ferromagnetic metallic (FM) phase of the parent La1.2Sr1.8Mn2O7 (T-C= 120 K) is suppressed by Nd doping (z), and a paramagnetic insulating (PI) state appears above z = 0.3. The FM phase is suppressed also by Ca doping (y), but a layered-type antiferromagnetic (A-AF) structure appears above y = 0.3. We have investigated the stability of the d(x2-y2) (or d(3Z2-r2)) orbital by Madelung potential calculation based on the structural data, and have found that orbital polarization governs the magnetic structure in bilayer manganites.