my iCloud storage is empty, but still it shows that it's full!

What is iCloud storage is described in the articles Introduction to iCloud - Apple Support

Apps and features that use iCloud - Apple Support

When you first set up iCloud on a device, iCloud storage is automatically turned on for certain apps. Some iCloud features are also turned on automatically. You can turn these on or off at any time and customise the settings for each device. 

you have turned off boxes for notes , mails , photos .....they have temporarily stopped syncing and no data from these applications will be shown in iCloud unless you turn on the boxes again , the cloud storage is shown full as it has exceeded the iCloud storage limit Check your iCloud storage on iCloud.com - Apple Support

If you don't want to buy higher storage plan first archive the iCloud data Archive or make copies of the information you store in iCloud - Apple Support

And then downgrade the storage plan Downgrade or cancel your iCloud+ plan - Apple Support

Only files should be saved to external hard drive Connect and use other storage devices with Mac - Apple Support

Read the article Other ways to back up and restore files - Apple Support

Use cloud-based services

Cloud-based services don't require you to connect an external hard drive to your Mac. For example, iCloudcan automatically store your photos, calendars, contacts, notes, passwords, and more. And it includes iCloud Drive, which can store documents, desktop files, and other files of your choosing. To access those files, you just need to be signed in to iCloud. Other cloud-based services are available from third parties.

Hi khatereh_k

We'd like to know more so we can try to help. Reply with the answers to these questions:

• How are you determining that the iCloud storage is calculated incorrectly?
• When you go to Settings > Your name > iCloud > Manage Storage, does each app not add up to the amount of storage iCloud is reporting as used?
• Does restarting seem to make a difference?
• Is storage calculated accurately if you log on to the iCloud site?

Best regards.