How to protect vps data from datacenter administrator

The data center admin has access to the HDD file. (VDI file or etc) How to access VPS data only by having root password and operating system(linux)?

Impossible.

The data center admin is looking from above the filesystem. If they want they could clone your system, and reset your admin password. All without you ever knowing about it. Not even encrypting the filesystem is going to help you here.

If you have data you do not want someone else to see you do store it somewhere else. On an external media or your own personal system. That way you can encrypt it making sure there is nobody able to see the contents.