Helo,

I own a Windows rust server on which I installed the rust server following this tutorial:
https://www.rustafied.com/how-to-host-your-own-rust-server

I have installed a server and I have 2 servers in a way that I have 2 'startservers.bat' file.
The servers are working properly only I have a problem that they have common plugins and I don't want that, means oxide is installed and everything is in the plugins folder share both two servers and I don't want that. Can that part be separated?

have one server in one folder and another in another folder. 

Yes but then I will have to install 2 servers or how do I do that? 

correct install to have 2 difrent

You can use the same RustDedicated install to run both modded servers, you just need to make sure each server has its own oxide folder, the way I do it is have each server's oxide directory inside its own identity folder.

+oxide.directory "server/IDENTITY/oxide"​

runescape

You can use the same RustDedicated install to run both modded servers, you just need to make sure each server has its own oxide folder, the way I do it is have each server's oxide directory inside its own identity folder.

+oxide.directory "server/IDENTITY/oxide"​

I understand that you have one oxide installed for each server. How to install oxide 2 times on the same server?
I now have a folder named "oxide". Can I copy that folder and paste it in another place and change his name to "oxide2" to be for another server?

I have one RustDedicated and one oxide for multiple servers, each server has its own oxide folder as I explained above.

In your start file add to the command

+oxide.directory "server/IDENTITY/oxide"​

change IDENTITY to your folder name of the other server in /server