Altium pad features and difference between Hole Size and "X-size and Y-size under Size and Shape"
Green portion represents the hole and grey portion represents the pad surrounding the hole for electrical/mechanical connectivity.

So in pad properties,


Hole Size: Specify the hole size. (It is advisable to increase the hole size by some percent to ensure smooth entry/exit from the hole)
X-axis: Size of the pad in x-dimension(left-right)
Y-axis: Size of the pad in y-dimension(top-bottom)


The value of X-axis and Y-axis will be same if your pad is circular, and different otherwise