[farshads83]

how can i calculate reynolds number in cube with three holes?
do i need hydrolic diameter for reynolds number? if yes, are holes taking account for calculating?
for expmple a cube with 300*300mm and three holes with 2mm radiuos how can i calculate?

[flotus1]

Based on your description, your flow has at least 2 representative length scales: the cube length 300mm and the hole diameter 4mm. Both length scales are valid for calculating a Reynolds number.
So the question should probably be: what do you need a Reynolds number for?
It is just a number, writing either one on a piece of paper does not change your simulation result