how do I refund money which one of our sub-contractor deposit to my company account by mistake.

Hi Butterfly8 

You may want to speak to your accounting advisor in terms of the process. However, if the payment was by mistake and it was refunded, my recommendation would be to just create a new Receive Money transaction from the deposit and then a Spend Money transaction from the withdrawal. This can be allocated to the same account so there will be no long outstanding impact on that account.