If your EE setup is hogging server resources either one or more of the following is happening:
- your server is not powerful enough for your demand;
- your server scripts are poorly written (what makes sense when you say the overload happens after cleaning the server cache), usual suspects are "stats" plugins, star ratings, and so on;
- your blog is under some kind of attack (xmlrpc.php, brute force, or other).
You should take a look at your logs in order to find out what's going on, what doesn't void the need of deactivating all plugins (but Nginx Helper and cache) in order to see if the issue gets some relief or not.
