解:法一、如圖,

$在Rt\triangle ABD中,\angle ADB=90^{\circ},AD=BD=3,$
$\therefore AB=\sqrt{A{D}^{2}+B{D}^{2}}=\sqrt{{3}^{2}+{3}^{2}}=3\sqrt{2},$
$\therefore \cos \angle ABC=\frac{BD}{AB}=\frac{3}{3\sqrt{2}}=\frac{\sqrt{2}}{2}.$
$故選:B.$
$法二、在Rt\triangle ABD中,\angle ADB=90^{\circ},AD=BD=3,$
$\therefore \angle ABD=\angle BAD=45^{\circ},$
$\therefore \cos \angle ABC=\cos 45^{\circ}=\frac{\sqrt{2}}{2}.$
$故選:B.$