Let's make sure you only gave a single account to access your QuickBooks company files, mahesh_s,
If you're using two separate email addresses fir the two company, the system will create distinct ID's to identify each account.
The best remedy for this is to invite the main company email that you want your accounts under. Say for instance, if Company A is using sample@sample.com email and you want it this login to be the main email of the two accounts, invite that email to Company B.
Here's how:
Go to Settings ⚙, then Manage users.
Click on Add user.
Select the user type you want to create. More options will appear on the screen depending on the user type you select.
Enter the new user’s name and email address, then select Save.