The duration between auto saves can be configured in of your Factorio Server settings, inside the config.ini file inside the config directory of your server. Use the Files tab as shown below to find the file.
Open the file by clicking on the blue pencil icon to the left of the file name. The file will open and will look like something like this:
We are looking for the key autosave-interval in this file. The number show after the = is the number of minutes between auto saves. The default is five, and you can change this to any other number of minutes.
Save the changes and restart your server after you have made your changes.