∵四边形ABCD是菱形,且AC=12cm,BD=16cm,∴OB= 1 2 BD=8cm,OC= 1 2 AC=6cm,AC⊥BD,∴BC= OB2+OC2 =10(cm),∵S菱形ABCD= 1 2 AC?BD= 1 2 ×12×16=96(cm2),S菱形ABCD=BC?AE=10AE,∴AE= 96 10 = 48 5 (cm).故选D.