Hello, We have receive payment from flipkart against various orders also they charged fees (commission) for the same. But we dont understand how to reconcile it.

I have a suggestion that can help you reconcile your account, @shraddha-h-londo.

You can add the commission fees as another line item when you process a bank deposit. This is to match the transactions you have and to reconcile the account.

Here's how:

1. Click the +New icon located in the upper right-hand corner.
2. Under Other, click Bank Deposit.
3. Select the Account and Date.
4. Under Select the payments included in this deposit put a checkmark on the payment we just added.
5. Under Add funds to this deposit, select the customer’s name from the Received from column.
6. Choose Bank charges and fees or any expense account from the Account drop-down menu.
7. Enter the amount. 
8. Click Save and close.

I'm including this sample screenshot for reference.

Once done, let's match the transactions by going to Banking, and clicking Match in the For Review section. You can also consult your accountant on how to categorise the transaction accurately.

I've added an article for your future reference when you're ready to assess your business income and expenses through QuickBooks Online: Reconcile an account in QuickBooks Online. This also includes how you can undo the process or fix errors.

Once done, you can always review the data by opening a Reconciliation Report. Just click the History by the account on the Reconcile page. 

I'm always here to provide help and answer any questions that you may have with your transactions. Keep safe always, @shraddha-h-londo.