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Server.cfg is a config file that lies in the ...cfg/ folder of the game or mod. It is a file that get's executed when a server is launched as dedicated. You can place a list of convars inside it for your server specific options that will get executed when the server is launched.

Note.png Note: 
Explain the operation in more detail.
* Server execute ...cfg/server.cfg file by default, on every map start.
* Console Variables inside the config file, values are reset back on map changes.
* You can change server config file to another, using cvar: servercfgfile

* However, games like Counter-Strike: Global Offensive, which have different game modes,
  each game mode use Valve's config files ...cfg/gamemode_*.cfg.
  So, there is a big chance one of Console Variables not work from server config file, because
  game mode is overriding that cvar setting.
  In CSGO, to override Valve's game mode setting, you use override config files.
  For example ...cfg/gamemode_casual_server.cfg

See also