Hello there, @rameet.

I'd be glad to help link the deposit to the open invoice in QuickBooks Online (QBO).

Once done recording the deposit in QBO, you must record a Receive Payment under your customer's name and use the deposit check as a credit on the invoice.

1. On the Receive Payment page, select the correct customer.
2. Under Outstanding Transactions, select the open invoice.
3. Look for the deposit created under Credits.
4. Click Save and close.
5. Once done, you can open the transaction list of your customer to check if the invoice was already paid.

You can see attached screenshots for additional reference.

To learn more about linking a deposit to an invoice, you may check this article: How to link a deposit to an invoice.

On the other hand, you can also check our Help articles for your future reference: Help articles for QuickBooks Online.

You can always add a post/comment below if you have any other questions about deposits or invoices. I'm always here to help you!