This article explains how to delete a secondary phone number from your Apple ID account on an iPhone.
Steps

Step 1. Open iPhone Settings
The icon looks like a gray gear and is located on one of the main screens.
It may also be in a folder called "Utilities"

Step 2. Scroll down and tap iCloud
It is located in the fourth group of menu options.

Step 3. Tap the email address associated with your Apple ID
It is located at the top of the screen.

Step 4. If prompted, sign in with your Apple ID

Step 5. Tap Contact Information
It is the first of the items listed under the Apple ID.

Step 6. Tap the phone number you want to remove

Step 7. Tap Remove Phone Number
Note: You are not given the option to remove a "primary" phone number. This means that the secondary number is the only phone number that appears saved in the account associated with the Apple ID

Step 8. Tap Remove
Your friends will no longer be able to use this phone number to communicate with you via Apple services such as FaceTime, iMessage and iCloud Sharing.