My company is classificated as Limited Liability Company (Ukraine).
I'd like to know how can I withdraw money from upwork to bank account of my company?
And if I can, will this procedure be legal? (I know this is OK for individual entrepreneurs and private enterprises)?
If your company's bank account is registered under your name, you can add it to your Upwork account and use it to withdraw your earnings. You'll need to speak with a local tax advisor or accountant in order to find the answer to your second question.